Down Time
by Lorr
Summary: Maybe it was one too many burned out planets. Maybe it was one too many friends lost. Maybe it was shouldering responsilibity for so many taken by the Wraith. Even his closest friends are beginning to wonder if Sheppard is succumbing to the pressure.
1. Chapter 1

**Title:** Down Time

**Author:** Lorr

**Genre/Rating:** Drama, H/C

**Characters:** Sheppard, McKay, Ronon, Teyla, Carter, Keller, Lorne

**Disclaimer:** The Stargate universe and characters belong to others. Wish it was me. I come here to play.

**Spoilers:** This takes place after Quarantine, but before Outcast. Some minor spoilers for episodes up through Quarantine.

**Warning: **None that I can think of.

**Note:** The story is a kind of sequel of another fic I wrote called Overload. I think I've put enough information in here, so it isn't really necessary to read it. I would love, though, if you did read Overload! Please note that I started this in February, 2008, so I didn't know what would happen in canon after that point.

The Ancient gene, and Sheppard's ability to use it to maximum effect, is pivotal. I wrote it because TPTB didn't really seem to feel the need to do an episode centered on it. Pity.

Reviews are always appreciated. Please be honest. Thank you for reading. I hope you enjoy it.

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**Chapter 1**

A dust covered MALP emerged from the wormhole and rolled to a stop on one side of the Gate room. It was closely followed by a dozen Marines, equally dusty and smudged with soot. As they moved out of the way, each turned to watch the rest of the away team come home. They were all visibly exhausted and looked like they'd been through hell. Sheppard and Ronon were the last to appear. A lieutenant broke away from the group of Marines and approached them.

"Sir?"

Sheppard waved him off. "I'll handle the debriefing, Lieutenant. Make sure everyone is checked out in the infirmary and gets some rest. Schedule a CIS debriefing tomorrow. Everyone goes."

"Yes, Sir." The young man paused for a moment before asking, "Can I take your gear?"

"Yeah. Thanks." Sheppard unclipped his P-90 and handed it over as a sergeant appeared to take the tac vest.

The two Marines turned and led the waiting men and women down the corridor towards the armory. They secured weapons and unzipped their tac vests as they filed out of the Gate room. A technician guiding the MALP followed them.

Sheppard and Ronon walked across to the foot of the stairs as Col. Carter and Teyla descended from the ops level.

"Did you find any survivors?" Sam asked, glancing at the last of the away team as they left. She already knew the answer. Not many.

The attitude of the whole away team was easy to read. They were sick at heart. They'd seen too many burned out worlds in the last few of weeks. One was too many, but they'd all been on more than one.

The settlement on M7R-892 was the last confirmed to have been destroyed by the Replicators in their rampage across the galaxy. Survivors were few and far between. There were some miracles, people living on remote farms, a few who escaped through the Gate or some who had been quick enough to find shelter sufficient to protect them. A couple of times, no-one was found alive.

"Only a handful. Total of 47 alive out of 3,700." Sheppard exhaled wearily. "They're on 721."

The refugee compound on M9P-721 was getting much more traffic lately. It had been set up to help relocate people needing to find a new home after Wraith cullings. Now they were using it to care for and relocate the all too few survivors of the Replicator campaign to wipe out the Wraith's source of food, humans. In some cases, the refugees were trading partners and friends, allowing for groups of survivors from different planets to be resettled together. Many either could not or would not return to their own planets. Fear and the destruction of families, homes and lives made it impossible.

"Any injuries that need to come here for treatment?"

"No. If they were close enough to get injured, they died." Sheppard replied. It sounded cold, but it was true. It was also merciful. Most injuries were agonizing and ultimately fatal.

"Is there nothing left?" Teyla asked, unable to hide her pain and bitterness.

"Nothing. The survivors are alive only because they were outside of town when the Replicators got there. They were in some caves, setting up stores in case the Wraith attacked."

"They were already searching for other survivors when we got there." Ronon added.

Col. Carter nodded grimly. "We'll find a safe place for them."

"Yeah." Sheppard's tone was flat, but she could hear a deep anger in it.

"Okay, you two know the drill." Sam glanced at her watch and decided the rest of this conversation should wait. The men standing in front of her looked like they were ready to drop. "It's almost 2100 hours. Infirmary first, then get some rest. Come and see me in the morning."

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"Did any of you get any sleep while you were away?" Dr. Keller asked as she examined Sheppard and Ronon. None of the away team looked as though they'd gotten more than a few minutes during the three days they were gone.

"Some." Sheppard replied without convincing her. The desire to get off yet another ghost planet had spurred the team to search almost without stopping. The only reason they would not need to go back was the fact the inhabitants, the few able-bodied still alive, had already searched part of the town. The remainder was done with life signs detectors.

"Right." Jennifer said skeptically. "Okay, I want you both to get something to eat then sleep. Now. No detours."

"Okay." Ronon slipped off the examination table.

She stared at Sheppard. "I mean it."

"Okay. Okay." Sheppard would have rolled his eyes if he weren't so tired. He dropped off the table and followed his friend out.

Repeating what had already happened with the entire away team, the two men walked silently down the corridor and parted for their respective quarters without a word. No-one was hungry tonight and they all needed to wash away the dirt and smell of destruction. Each of them just wanted to block out the last 72 hours, and all of the ruined towns and people they'd seen since the Replicators were unleashed. More than a few silent prayers of thanks were said now that the Asurans were now dust themselves.

Sheppard stopped just inside the door of his quarters, needing to sleep but wary of what would inhabit his dreams. He finally took a deep breath and began to strip off, suddenly wanting nothing more than to feel clean, to smell something more than burned out towns and decomposing flesh. He punched the stereo on button but didn't really hear the music. It wasn't loud, but it was noise other than crying.

The jets of hot water pummeled his skin, scrubbing off the grime. Leaning on outstretched arms, he stood with his head bowed so that the full force hit his neck and shoulders. After several minutes, John straightened and reached out to grab his toothbrush and paste. A moment later, he tossed the tube into the sink. It was only the metallic tang of blood that told him he'd tried too hard to scrub the taste of 892 out of his mouth.

He turned off the water and dropped the toothbrush next to the tube. His body felt marginally better, but the need for sleep was too great. After barely toweling off, John found a pair of loose track pants and pulled them on. He didn't remember flipping the covers off the bed and falling onto it. Blackness descended and he was asleep.

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John sat up suddenly, blinking into the dimness of his quarters. He rubbed his eyes and searched the room again. Trying to figure out what woke him, he took a deep breath and exhaled it slowly. He didn't remember dreaming and all was quiet. Was it time to get up? It was still night and only the light from the smaller, more distant moon shining weakly through a thin cloud layer illuminated his quarters. He glanced at his wrist and realized his watch had been discarded along with his clothing earlier. The disc changing on the stereo made him turn. The display told him it wasn't even 0100 hours. He'd been asleep less than three hours.

John rolled off the bed and walked to his desk. He picked up and turned on the radio left there for emergencies. A few minutes of listening to the mundane, late night traffic told him nothing was amiss. With a low groan, he dropped back onto the bed and closed his eyes again.

The next time he woke the stereo clock showed 0520. He looked around and listened intently. Again, there were only the normal sounds of Atlantis, the low music, the ocean far below and…nothing. After several seconds, John shook his head. Dreaming, must have been dreaming, he thought to himself.

Despite feeling like he'd gone ten rounds with both Teyla and Ronon, he decided it just wasn't worth trying to get more sleep. Stiff muscles protested when he got up and headed to the bathroom. Maybe a short run and another long, hot shower would help.

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Col. Carter was surprised when Sheppard walked into her office. It was 0630. She had a large mug of coffee and a bowl of fresh fruit salad sitting next to her laptop. "John? I didn't expect to see you this early. How are you?"

He half shrugged as he dropped into one of the chairs opposite her desk. "Fine."

She bypassed the fact that it was a less than truthful statement. He looked like he'd been through exactly what he'd been through the last few months. She decided not to press it. "The Apollo will be here tomorrow."

Sheppard blinked in surprise. He'd lost track of the days. "Already?"

Sam frowned, knowing he was aware the Apollo was well on her way back to Atlantis when he left on his last mission. She quickly replaced the frown with what she hoped was a pleasant smile. "The repair crews on Earth had plenty of time to assemble the needed parts. They've been getting a lot of practice the last couple of years."

"Yeah." He nodded sideways in wry agreement. "What about the Daedalus?"

"She'll be ready in a few days, but the SGC wants her to assist in a mission. She won't be heading back to Pegasus for at least another week to ten days."

He exhaled heavily, knowing better than to ask about the mission. "Well, it looks like the Wraith are still busy picking teams. If we're lucky, it'll be a little quieter around here for a while without the Replicators."

"We can only hope. The fact that some of the Hives don't have queens is a plus." Sam raised her eyebrows thoughtfully. She paused for a moment, taking a sip from her mug to fill in the silence. "John, I think this is a good time to let Rodney install the streamlining program he's been working on. We don't have any teams off-world at the moment except 721 and the alpha site, so this might be our only opportunity for a while."

He abruptly scratched the back of his head, staring at the floor in thought.

"John?"

His head snapped up, a sheepish expression on his face. "Uh. Sure. He said it'd be offline for only a couple of hours, didn't he?"

"About two." She looked at him a little more closely. It wasn't difficult to see he was tired. The last few months had been hard on everyone, but perhaps more so John. He'd taken responsibility on himself for many events that may or may not have been his. Along with the almost non-stop pace they'd been keeping, it was a lot for anyone to bear. "He's been tweaking it while everything else was going on for the last couple of weeks."

"Why does that worry me?" His eyes narrowed a fraction. "When?"

"Tomorrow. Once the Apollo is in orbit, and right after we report to Earth." She chuckled silently. "Don't worry, I've gone over it with him. Meantime, I think you and Ronon, and your team from this last mission, should stand down for several days."

"I've scheduled all the teams that have been on search and rescue to have a week on base with days off and light training."

"You and Ronon, too, John." She knew he'd missed the point, purposely or not. "It's been a hectic couple of months. Take some time."

"It isn't necessary."

Sam shook her head once, a knowing glint in her eye. "Well, you have no option. Besides, Dr. Keller says she wants to run a complete physical on you."

He exhaled heavily. "Great."

xxxxxxxxxx

"Col. Sheppard." Jennifer Keller studied his face with a critical eye. Even though she would have expected he would still be tired, he appeared to be much less rested than he should. "How are you feeling today?"

He shrugged. "I'm good. Col. Carter said you wanted to see me, something about a physical?"

"Yes, it's been nine months since…well, since you were shot." The young doctor swallowed in discomfort, not wanting to actually say that it had been nine months since he'd been forcefully drugged and manipulated into almost destroying Atlantis. It was determined that he should have a complete physicals every three months for a year, just to be sure there were no long term effects from the experimental drugs and treatment he'd received. After that, annual physicals, in combination with the post mission exams, would suffice. She frowned, checking the notebook cradled in her arm. "I have a pretty full load at the moment. Would this afternoon be okay?"

"Sure." John was only partially relieved at the delay. "What time?"

"How about two o'clock?" She smiled.

He shrugged disinterestedly. "Sure, no problem."

"Thank you Colonel. I'll see you later." She watched him leave before turning back to her patients.

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"How's it going, Rodney?" Col. Carter looked over his shoulder at two computer screens. The chief science officer had been working on the laptops simultaneously, and grumbling none too quietly for the last hour and a half. "Everything alright?"

His face scrunched up as he pointed to one screen then the other before typing again. "Well…I thought. No, no. Everything's okay."

She looked at the screens more closely. He wasn't working on the upgrade. Instead, he seemed to be going through part of the programming in the city's systems.

"Thought what?" She pressed.

McKay wiggled his fingers at one of the screens then rubbed his eyes. "I'm just tired. I was verifying some of the settings when it, well, when I thought, for a split second, the program changed."

The colonel's eyes narrowed as she leaned in a little closer, reading the displays more thoroughly. "Changed? What changed?"

"I said thought, and I said tired. I've been working almost nonstop when we haven't been busy with the Replicators and Wraith." He threw her a look of impatience. "It's fine. I've gone back over the code and it's fine."

"Okay." She said evenly as she straightened. Sam knew better than to respond to Rodney's mood. Instead, she suggested, "We can postpone for 24 hours."

"Postpone? Why? There's no need to postpone." He sputtered in surprise at the thought of it. "Everything is pretty much ready. I just have a few small tweaks to make."

Sam decided to leave it at that. Everyone was exhausted and getting a little squirrelly. The need for down time was more than apparent, especially with long timers. She was determined to make sure everyone on the base took at least a few days off over the next two or three weeks. The question was who needed it most and who could wait?

She turned and walked to her office, making a mental note to talk with Zelenka later in the day. He'd been working on the project, too, and knew the Ancient systems almost as well as McKay. As much as she trusted the chief scientist, it would be unwise to just dismiss the incident, real or imagined.

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Sheppard stared at the gauze covering the needle marks in the crease of his left elbow. He was certain the infirmary technician who drew the umpteen vials of blood was new to the business. It took him three attempts to find the vein. He was all apologetic, but the colonel was not in the mood. Finally, the nervous young man found the vein, got what he needed and scurried out.

"Colonel?"

He looked up to see Dr. Keller watching him with concern in her eyes.

"Are we done?" He moved to get off the exam table.

"No, no, not quite." She stepped back. "We just have the scan left and then we'll be finished."

"Right." John slid off the table and followed her to the scanner. He stretched out on the bed and silently waited for the test to be completed.

A few minutes later, Jennifer powered the machine down and walked over to Sheppard. "Okay, now we're all finished. So far, everything looks good, but I'll…"

"Let me know. Thanks." He finished for her as he abruptly got up and walked out.

He left her standing, mouth open. Sheppard was rarely dismissive and never flat out rude. Something was up. She slowly returned to the scanner controls and sat down. It was some time, though, before she began reviewing the scan results.


	2. Chapter 2

**Chapter 2**

"Colonel, you're just in time." Col. Carter smiled at Sheppard as he walked into the operations area then nodded at Chuck. "Dial the Gate, please."

"Yes, Ma'am." The technician began pressing the symbols on the console. Seconds later, the wormhole opened. They waited, knowing the SGC was going through the same process. After several minutes, he said, "We're through to Midway, Colonel."

"Midway, this is Atlantis. Do you copy?"

A disembodied male voice replied. "Atlantis, this is Midway. We're waiting for the SGC to dial in, too."

Having both planets dial in at once wasn't an unusual procedure. As was the case tonight, sometimes there was a transfer of personnel and supplies. Tonight, a handful of personnel were returning to Earth after their stints in Pegasus. Since they needed to spend 24 hours on Midway, there was no need for the wormhole to go all the way to the Milky Way. The station, in turn, was getting a delivery of food and equipment from Earth.

"Good to hear. How are things going there?" Sam was happy the bridge to Earth was working as well as they all hoped. Not needing the ZPM for the long journey or to keep in regular contact with the SGC was more than valuable.

"Fine, thank you, Colonel." The voice replied. "We have a wormhole coming in from the Milky Way now."

A few minutes later, the departing personnel disappeared through the event horizon. The data transfer was lightening fast.

"We'll dial in as soon as we're on line again. It shouldn't be more than a couple of hours."

"We copy, Colonel. Good luck."

"Thank you. Atlantis out." With that, the Gate shut down. "Apollo, we're taking the Gate offline."

Ellis responded. "Acknowledged."

Col. Carter turned to McKay. "Rodney, you can run the program now."

"Finally." He muttered with annoyance. He snapped his fingers several times at the people around him then hunched over his computer and began typing commands. Sitting nearby, Zelenka was also typing furiously, occasionally glancing at McKay. Two minutes later, McKay looked up at the two Colonels. "I'm ready."

Sam slipped into a chair at one of the computers and nodded her head. "Okay, let's do it."

McKay turned to his laptop. "Right. Taking the Gate offline in three, two, one." With great exaggeration, he pressed a key on the console next to his laptop. Everyone looked around in expectation, and back at him when nothing happened. "Well, what did you expect, fireworks?"

Without another glance around, the chief scientist began entering more commands into his laptop. Sam on one side with Radek and nearly a dozen technicians on consoles and laptops around them peered at monitors and screens, closely watching the installation and functions of the city's systems.

Sheppard, a vague uneasiness nagging at him, decided to stay in the vicinity. He watched McKay's computer screen and the Ancient monitors as work progressed. Occasionally, he would stop by during such a project, but today's undivided attention was unusual. Twenty minutes into the process, McKay turned and glared at him. "Is there a problem?"

"No." John glanced at him then back at the screen. After a moment, he turned and walked away.

Sam, observing the exchange out of the corner of her eye, was tempted to ask her 2IC what was worrying him, but decided against it. Having the Gate offline for even a minute was a little scary for everyone.

Slightly more than two hours later, McKay dialed the Gate. The address he input started the macro sequence that would connect them to the Midway station. Everyone in the Gate room held their breath until the wormhole was established, but they only relaxed later, when the technician on Midway dialed Atlantis, confirming the system was online and fully functioning in both directions.

No-one seemed to notice Sheppard disappear down the stairs at the far side of the control room deck.

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"This is ridiculous." Sheppard grumbled as he got up. It was the third night in a row he'd woken with the distinct impression something was out of place. He glanced at his watch. 0217 "What the hell is going on?"

He picked up the radio and turned up the volume. Tonight, he'd left it within easy reach. After listening to the various frequencies used in the city for several minutes, John decided that all was safe and quiet. He also decided that maybe Carter was right. They all needed a break.

Instead of turning the radio off John turned the sound down to just audible again and put it back on the cabinet next to the bed. He rolled onto his back and took several long, deep breaths, trying to dispel the unsettling feeling that persisted. After fifteen minutes, he got up, dressed and left his quarters. The only way he was going to get more sleep tonight was to take a quick look around.

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Col. Carter disliked the necessity of conducting meetings with her chief medical officer and the base psychologist. She understood the need to keep a close watch on the physical and mental health of the people under her command. They were in a galaxy millions of light years from home with only a couple of ships and a small bridge connecting them with help. Those facts did not make the briefings any more palatable.

She smiled at Jennifer Keller and the interim replacement for Kate Heightmeyer, Beth Reynolds. Dr. Reynolds was quite different to Kate. She was tall and big boned with graying red hair, and had a warm, straightforward demeanor. The contrast to the lost psychologist was both disconcerting and welcome. They did not need daily reminders of their friend.

Beth came fully briefed about the unique situation in Pegasus. She had been consulting with the SGC on personnel that would be suitable for deployment here, so she was familiar with the files of current and past expedition members and all mission reports. She'd also been a friend of Kate Heightmeyer, so she understood the impact of her death. Beth would remain on Atlantis until a more permanent replacement was found and brought up to speed.

The Atlantis commander looked at Jennifer. "How are things in the infirmary?"

She took a deep breath before speaking. "Apart from a broken arm and some bruises and scrapes from recent missions, the worst case I have right now is an emergency appendectomy."

"Appendectomy?" Sam raised an eyebrow.

"Sgt. Turner." Jennifer responded. "The surgery was last night, and he's already up and around."

"Nothing else?" Sam felt there was something more.

A slight frown creased Jennifer's brow. "There have been a few more cases of minor illnesses than normal, some signs of sleeplessness and loss of appetite. I'm keeping a close eye on it, but I'm sure it's nothing serious. I think we're all just a little tired." The frown disappeared. "The time off you ordered will give everyone some breathing room."

"I thought it might help." Sam turned to the psychologist. "Have you seen anything we should be concerned about?"

"The critical incident stress debriefings are going well." Dr. Reynolds barely glanced at the data pad on her lap. She brought it out of habit even though she knew all of the information it contained. "There are some signs of stress, and a few people could use a couple of weeks back on Earth, but most are quite doing well. Better than one might expect, actually."

Sam nodded. "A lot of that is due to you and Kate. It's also a pretty tight-knit group. Most of them were stationed at the SGC before coming here, which helped them understand what to expect."

"Thank you, Colonel." Beth acknowledged the validation of her contribution. "Having good commanders and support on the ground has a lot to do with it, too."

"I inherited a good team." Sam said with sincerity. "You'll keep me informed of any concerns you have?"

"Definitely. I'm preparing a complete report for you. I'll email it later today." Beth said as she and Jennifer stood up. She didn't move, though. Piercing eyes studied the colonel's face. "What about you? When will you get a few days off?"

The question caught Sam by surprise. "Um, well, soon."

"Yes, Colonel. Soon." Dr. Reynolds said with an unreadable expression, as she and Jennifer turned to leave the office.

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Maj. Lorne waited patiently for his commanding officer. He knew Sheppard was supposed to be relaxing for a few days, but apparently the lieutenant colonel thought differently. Instead, he was sitting at a computer in one of the labs doing…something. Evan caught a glimpse of what he thought were schematics of the south pier of the city.

"Colonel?"

Sheppard blinked, suddenly realizing that he was waiting. "Sorry. I want everyone with the gene to get in at least six hours of flight time, including two hours flying formations with three other Jumpers. They also need a couple of hours in battle simulations."

"Sir?" Lorne wasn't sure where this was coming from. All Air Force and Marine personnel with the Ancient gene were thoroughly trained on the Jumpers as soon as they came to Atlantis. Civilians, however, were generally given an hour or two of practice, just enough to enable them to get from point A to point B without crashing.

"After what happened in the asteroid field, I want to be sure everyone on this base has half a chance of protecting Atlantis if we're ever cut off again." Sheppard replied firmly. "After the initial training, everyone is to have at least an hour flying a Jumper once a month."

Reasonable enough, Lorne thought, even though it was highly unlikely that Atlantis would be caught so short on pilots again. He was more curious about the colonel's sudden need to beef up the already more than adequate security of the city. This was the third order in three days he'd come up with. First, he increased the number of graveyard watch patrols by one quarter. Yesterday, he pulled a spot inspection of the armories, a first, and decided they needed more heavy small arms near the Gate room.

"Yes, Sir. I'll have a schedule for your review tomorrow."

"Thanks."

The major left Sheppard completely engrossed in studying the schematics. He frowned deeply as he walked down the corridor. Everything was entirely reasonable considering the chaos and loss of recent months. Why did it feel that it just wasn't quite right?

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Beth Reynolds' office was near the one that had been used by Kate Heightmeyer, but different in layout and décor. Beth scavenged the most comfortable chairs and sofa she could find in the city and arranged them almost as a sitting room. Even though her stay on Atlantis would be relatively brief, she brought some of the comforts of home. Colorful pillows and a large Persian rug added warmth to the room's neutral tones.

She sat on the sofa, her laptop sitting on a well used wooden lap desk resting on her knees. The file notes she was typing were momentarily forgotten as she stared at the door. John Sheppard had been the last appointment of the day. She knew him from interviews conducted four years previously at the SGC, and more recently during the brief return of the Ancients to Atlantis. Everyone working on the Stargate project on Earth was thoroughly vetted. Even though danger and death were experienced by military personnel on Earth every day, the added secrecy and utter strangeness of the work at the SGC required more of every individual involved. Personnel sent to the Pegasus Galaxy needed to be on a level of their own.

Sheppard was unceremoniously dropped into their weird little universe without any warning. Going from the snug, safe mindset of being the only intelligent life forms anywhere to Stargates and aliens and hyperspace was usually afforded time and preparation. They'd all been concerned about his reaction to it, some more so than others. He surprised even her, though, and took to it like he was born to do it, spending the few short weeks before the expedition left absorbing everything thrown at him. At the same time, Sheppard spent as much time as possible in the chair at the Antarctic outpost, pulling enough information out of the Ancient database to keep the scientists busy for months or years.

The two meetings Beth had with him since arriving and Kate's file notes only reinforced her initial assessment of Col. Sheppard. He had a rock solid core that allowed him to keep functioning at an extraordinarily high level no matter what the circumstances. He did it with a deceptively laidback demeanor. But, now, for the first time, Beth was worried.

She knew that, despite the face he showed the world, John felt things deeply. It fueled his need to protect people. She was certain recent events would have shaken him. He thought he was directly responsible for Kate's death and, to a large degree, the losses of Elizabeth and Carson. Add to that his hand in the circumstances of Wallace's death at the SGC and the vicious rampage of the Replicators and Wraith on the humans in Pegasus, and the load was crushing.

Even if reserved when it came to giving details about himself, his feelings, thoughts or past, John was a relaxed individual. This evening, however, the discussion was very different. His normally charming, yet thoughtful, manner was missing. He was tense and distracted. Her gentle questioning received only, "I'm fine" as a response.

Beth blinked and looked down at the laptop. It was in sleep mode. She logged in again and read the last entry. It was about a discussion with Sam Carter earlier in the day. The colonel was concerned with the perceptible change in Sheppard since his return from the search and rescue mission on M7R-829.

The psychologist thought about it for a long time before adding a final few sentences and logging off again. He was the last person in either galaxy she thought might lose his way but a fear of the cumulative effect of the brainwashing, for want of a better word, and the events of the last few months was beginning to take root.

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"This is the second time in three days." Ronon growled. He'd waited as long as he could, which wasn't very long at all. He stopped prowling around the workout room and looked at Teyla, who sat on the bench against the window. "You hungry?"

She was, actually. The baby growing inside her made her almost constantly hungry. "Are you sure he agreed to spar today?"

"Yes, I'm sure." He helped her up. "I don't know what's going on, but he's acting kind of…"

"Distracted?" Teyla finished as they left the room.

"I was going to say weird. Haven't you noticed?"

She sighed. "I have hardly seen John since you returned from the last mission. However, I agree. He did seem quite preoccupied when I spoke with him earlier today."

"Do you know what's going on?" They stepped into a transporter.

Teyla responded as they exited near the mess hall. "I only know that he has been busy implementing new security measures in the city."

Ronon grunted. "He's supposed to be standing down for a few days. Carter ordered it."

"I know. He may just be taking the opportunity to increase security." She said even though she was not convinced.

"It's more than that. He's jumpy, worried about something."

"Jumpy?" She glanced up at him quizzically. That was not a word she would normally associate with John. "Have you asked him about it?"

"Yeah. He dodged the question."

"I will try to talk with him." The entered the mess hall.

"Good luck." He was skeptical. They both knew it was highly unlikely she'd get an answer.

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The vague feeling that he was waiting for another shoe to drop nagged at the edge of his mind and would not go away.

Sheppard stood at the window in his quarters. It was still more than two hours until sunrise and the world was dark. He missed the spectacular starscape on Lantea. The perfect clear skies, unpolluted with light and smog like Earth, was breathtaking. Even after three years, he hadn't tired of it. This new planet was equally unpolluted, but had a very different perspective of the galaxy. It was still impressive, just not quite as much as their previous home. At least so far, the view was also obstructed by clouds more often than not. He'd have to wait through a full year before passing final judgment.

He rubbed his right temple in hopes of easing the ache that had been there for days as he walked back to his desk, sat down and checked the city's defense plans one more time. Short of having a full complement of ZPMs, a couple more battalions of Marines, rail guns on every other balcony and several of the new Asgard plasma beam weapons, there was nothing else he could do to protect the city from attack. Training a back-up or two for the weapons chair might help, but there weren't enough drones or the power to waste, and no-one would come close to his accuracy. His innate ability to use the Ancient technology was unique. Being special was sometimes a royal pain in the ass.

With a deep sigh, John shut down the computer and went back to bed. He needed a little more sleep before meeting Ronon for the sparring session he'd promised the last couple of days. He was going to pay dearly for ditching him twice in a row. The Satedan was not particularly happy with him.

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McKay sat down at one of the computers in the control center, a coffee mug in his left hand. The diagnostic program that had been running for a couple of hours was nearly finished. Some kind of minor error in the city's operating system appeared two days ago, causing a few intermittent shutdowns in non-essential functions. Of course, it was nothing to do with the streamlining program he loaded three days before that. The Gate worked perfectly when they dialed earth every day since, as well as when Earth dialed in. He sipped coffee as he watched the results begin to scroll by on the monitor.

Without warning, the consoles around him went down. Glaring at the technician sitting nearby, he demanded, "What did you do?"

The young man frowned at the controls then looked at him. He held up both hands. "Nothing, Sir. I didn't touch anything."

The astrophysicist spun around, looking at everyone in the control room in turn. Every Ancient console and screen was dark. They all shook their heads, hands up in denial of wrongdoing. He turned back to his laptop and started typing rapidly.

"Dr. McKay?" The technician watched him, not knowing what to do.

"What? Can't you see I'm…" He stopped typing and stared at the screen. "No-one touch anything!"

Col. Carter came out of her office. Only light from the late afternoon sun and the minimal emergency lighting illuminated the space. "Rodney? What's going on?"

His eyes remained on the screen, watching data scroll by too rapidly to read. "I don't know. I was just running diagnostics to determine what's been causing the malfunctions."

"Are we in lockdown again, Doctor?" One of the other technicians asked.

McKay shook his head as he kept typing. "No. No. I…I don't think so. It's almost as if…" He reached out and placed his hand on one of the ATA pads. The control keys glowed momentarily then darkened again. He pressed harder and stared at it, trying to will it into life. It came online. With a loud exhale, Rodney took his hand away, only to see the controls go dead again.

Sam looked at one of the technicians she knew had the ancient gene. "Try that one."

The young man took a deep breath and put his hand on the pad. It came to life for barely a second even though he kept his hand on the pad. He closed his eyes in concentration, but it remained inactive.

"Rodney?" Sam walked around and sat at another laptop.

"It's the city's operating system. Something's wrong." He added before anyone could ask, "No, I don't know why and I'm working on it."

"Okay. We'll figure it out." She fervently hoped it was a very temporary glitch and that everything would be up and running again in a few minutes. As those minutes ticked by, though, Atlantis' commander and chief scientist grew certain that it was far more serious than an easily fixed glitch. "Could it be a problem with the ZPM?"

"No, no. The ZedPM is fine. We have plenty of power." He stopped typing to point at a graph on the screen. "This was just before everything shut down."

A few minutes later, a Marine lieutenant approached. She touched the transceiver in her left ear. "Col. Carter, we're getting a lot of radio traffic on the emergency channel. It looks like the Ancient systems are down all over the city."

"Thank you, Lieutenant." Sam barely glanced up from the laptop. "Tell them we're working on it. Unless there's an emergency, everyone should just sit tight for now."

"Wait, wait." McKay snapped his fingers. "We need to find out if anything in the city that needs the Ancient gene is working."

"Can we use the city wide comms?" Sam asked as she turned to Chuck. "Try it."

The technician pressed the control, but nothing happened. He tried again, and shook his head.

"McKay, this is Sheppard." The colonel's voice sounded in their transceivers.

McKay tapped his transceiver. "Yes, I know. There's a problem."

"What kind of problem? What's going on?" It was obvious Sheppard was not happy.

"I don't know, exactly. It looks like the Ancient technology is offline."

"I know that. Is it another lockdown?"

"No. It's not a lockdown. We obviously have communications and it looks like none of the doors are locked." McKay continued pounding on the keyboard as he spoke. "Look, I don't have time to talk right now.

"Where are you, John?" Col. Carter asked.

"Out on the south pier. You're in the control room, I take it?"

"Yes. We're trying to determine what happened." She responded.

McKay placed his hand on the ATA pad again. This time, nothing happened. He muttered under his breath then spoke aloud into his comm. "I…we need you up here. Now."

"In a minute." Sheppard spoke again. "Colonel, we should be on alert."

"You read my mind." She responded.

"Maj. Lorne, all command personnel, go to channel four." There was a chorus of "Yes, Sirs". Col. Carter knew that her second in command was implementing the emergency plans for safeguarding the city. A minute later, Sheppard spoke again. "Colonel, I'm sending up reinforcements to secure the Gate room."

Almost immediately, two squads of Marines took up positions around the Gate. Minutes later, even more Marines appeared, carrying weapons ranging from P-90s to heavy machine guns. Knowing full well that the iris was also offline, everyone in the control area breathed a small sigh of relief at the added protection.


	3. Chapter 3

**Chapter 3**

Thirty minutes later when Sheppard arrived with Ronon. The handgun strapped to his leg was out of place over his civilian clothes. They stopped on the Gate room floor just long enough to check the security set up before climbing the stairs to the ops deck. Both were out of breath and sweating from running halfway across the city then up the nearly seventy flights of stairs.

"What the hell's going on?" John got out between gulps of air. He looked from Sam to Rodney then back again.

McKay jumped in immediately. "The Ancient technology is offline."

"We're not sure." Sam added.

McKay threw her a glance. "We can't initialize any of the Ancient systems." He paused. "Well, I could for about three seconds, but as soon as I took my hand off the ATA pad, it went dead. Now, nothing."

"John…" Sam started, but he was already walking around a console with one of the activation pads.

Sheppard rubbed his right hand on his hip and took a deep breath. The concern on his face eased only slightly as the console came to life as soon as his hand touched the pad. The large screen behind him glowed and data began to scroll down its length. It became lifeless again as soon as he backed away.

"Well, that's a lot of help." McKay muttered and turned back to the laptop. "Do it again."

Sam nodded and watched her laptop. Sheppard repeated the move, this time leaving his hand on the pad as McKay worked as fast as he could. He finally waved Sheppard away. Again, the console died.

"What happened?" John asked as he moved so that he could look over their shoulders at the screens.

"I don't know. It looks like it's the operating system. The problem is that we just can't get into it while it's offline." Sam replied slowly, thinking she was beginning to understand.

"Look, much of the Ancient technology needs someone with the gene to initialize it. Once initialized, all but a few functions run until turned off." McKay explained.

"I know, Rodney."

"Well, right now it isn't staying initialized, it's turning off as soon as we end contact with the ATA pad, and we can't get any of them to perform any functions." McKay reached out to the console with an ATA pad nearby and put his hand on it. This time nothing happened. "Half a dozen of us have tried to get anything to do more than light up, without luck. As far as we know, you're the only one that's been able to get it to actually work."

Sheppard frowned at him, not quite sure were he was going. "So? How does that help?"

McKay exhaled heavily, expressing his impatience. "We need the system running to find out what's wrong."

"John, we don't know what the problem is." Sam decided to take over the explanation. "We need to look through the program code to determine what's gone wrong and restore it. You seem to be the only person that can activate the system."

He started to walk back to the console. "Okay."

"No, no. That's not going to be enough. These controls just aren't going to give us the access to what we need." McKay stood up, looking around at the dead consoles. He suddenly snapped his fingers several times and pointed at Sheppard. "The chair. You can initialize the entire system and keep it active from the weapons chair."

"How long will it take?" Sheppard asked, suspecting an answer he wouldn't like.

"I don't know!" McKay snapped. "We have to figure out what's wrong first."

"Can't you just do the same thing you did on the Daedalus when the Wraith virus took over? Wouldn't it be easier to wipe the system and load a back-up?"

The astrophysicist closed his eyes and shook his head in frustration. "No, the systems here are far too complex and we don't know what the problem is yet."

Sheppard compressed his lips in thought then pointed towards the Gate room floor. "What about the pedestal Helia used?"

McKay shrugged. "We tried it, but couldn't get it to rise. You may have more luck."

Sheppard sprinted down the stairs but hesitated for a split second before trying to raise it, remembering what he had done the last time he used it. The near destruction of the city at his hands haunted him. He swallowed as he held his right hand parallel to the floor. A long moment passed before the small control pedestal appeared. He laid his hand on the pad and looked up at ops level.

"Anything?" The colonel asked loudly.

"Stand by." McKay's voice shouted back. Several minutes later he answered. "It isn't enough."

"Damn it." Sheppard muttered under his breath as the pedestal disappeared into the floor. He climbed the stairs two at a time.

Sam looked up from her laptop and shook her head. "It wasn't stable enough to really do anything. I think we have to see if the chair will give us better access to the system."

"Okay. Give me a few minutes to get down there." He turned and headed back down the stairs.

Ronon watched him disappear then looked at Col. Carter. She nodded and said, "Do you mind?"

"No." He hurried to catch up.

When Ronon fell in beside him, Sheppard said, "You don't need to come. It's just going to be boring."

"Nothing better to do." The Satedan half shrugged and kept walking.

As they reached the corridor leading to the route back down the tower, a group of technicians carrying portable lights, a naquada generator and other equipment passed on the way to the Gate room. It was now lit by the early afternoon sun, but would soon be in shadows. Similar equipment was being set up in the infirmary and the mess hall. They were grateful the late spring weather was warm enough to be comfortable day and night.

Sheppard's mind was racing as he and Ronon ran down the stairs. He'd felt nothing in the Ancient systems. The familiar sensation of knowing how the technology was reacting to his touch was absent. It was like Earth technology. Flip the switch to turn it on, cold and lifeless. Right now, the only way he knew it activated was because he could see it.

xxxxxxxxxx

Sam turned to Chuck. "See if you can get a signal to the Apollo. We need to get her back here."

"Yes, Ma'am."

A few minutes later, Chuck spoke quietly. "It's Col. Ellis, Ma'am."

She nodded and touched her transceiver. "Col. Ellis, this is Carter."

"What can we do for you, Colonel?"

"How fast can you get back here?"

"About ten hours. What's wrong?"

"All Ancient technology in the city is offline and we don't know why."

"We're on our way." He said without hesitation, knowing she wouldn't ask unless absolutely necessary. There was a pause. "Do you have the Gate, sensors, anything?"

Sam glanced at Rodney, who frowned and shook his head. "Nothing right now. We're blind."

"Sitting ducks." Rodney groaned miserably.

"We've barely been able to activate individual controls, and haven't been able to get any functioning." She glanced at her watch, wondering how long they would be vulnerable. "Can you check your sensors for us?"

"As we speak." Ellis responded. There was a pause. "Nothing in your vicinity."

"Thank you, Colonel. One more thing." She glanced at McKay. "Would you contact Midway for us? Let them know our situation and that we don't think they should try to dial in until we know more."

"Do you think it might be dangerous?"

"Probably not, but I want to be sure."

"Understood. Will do."

"Thank you, Colonel. See you in a few hours."

"We'll get there as soon as possible." Ellis signed off.

At least they knew the Apollo was on her way. She might not be able to protect them from a concerted attack, but she could be their eyes and ears.

McKay impatiently tapped his transceiver. He was impatient. "Sheppard are you there yet?"

"Not yet, Rodney." Sheppard snapped back. "Remember, the transporters aren't working."

xxxxxxxxxx

Two Marines were prying open the door as Sheppard and Ronon ran up the stairs near the chair room. Their flashlights helped the small amount of emergency lighting in the corridor. The pair slowed, gasping for breath as they walked into the room. Even though the trip from the Gate room was downstairs, they'd descended quickly then ran full speed from the central tower to the one housing this room. Sheppard looked around as he as he approached the chair. He was so accustomed to the city responding instantly to his presence that the darkness and silence were disturbing.

"We're here. Let's see if this works." He said as he sat down and placed his hands on the ATA pads. He breathed a sigh of relief and closed his eyes when the chair activated. It reclined but remained motionless. Lights in the room came on. "What do you need, Rodney?"

"We need access to the operating system." There was a pause. McKay was almost apologetic when he spoke again. "Uh, all of it. We don't know where the problem is, if it's systemic or isolated in key areas. Sorry."

"Great." Sheppard muttered to himself and inhaled deeply. He tried to relax as he exhaled. He was able to fly and land the city with the handicap of a single ZPM. Even if Atlantis felt lifeless, how hard was it going to be to keep the lights on for a while? He whispered, "Everything. Alright."

The city came to life. After that, it was impossible for Sheppard to know with certainty anything was happening. He felt nothing. The action was going on high up in the central tower, where who knew how many people were frantically searching the operating system for a bug, or bugs, big enough to bring the city to a standstill. He relied on their conversation coming through his transceiver to tell him it was working.

Ronon motioned for the Marines to continue their patrol. They quietly left as he moved a chair so that he could see anyone approaching the door as well as keep an eye on his friend. He had a feeling Sheppard was right. This was going to be boring.

xxxxxxxxxx

"I'm in!" McKay said with satisfaction. He glanced at Sam, who just nodded as she focused on her computer screen.

"Me, too." Zelenka and several other scientists and technicians chorused. Each was assigned a specific area of the system to search while they waited for Sheppard to reach the chair room. McKay and Carter would concentrate on those parts of the programming that governed activating and keeping the city's main operating system running. Zelenka had the Stargate programming. Everyone else had…well, everything else.

"Okay, you all know your assignments. Look, don't touch. If you find anything, just let me know." McKay used his most forceful tone. It was loud and clear that anyone who tried to dabble in repairs on their own would have their head handed to them on a platter.

The next few hours passed with growing frustration and doubt. It was immediately clear that someone had more than tampered with the programming.

"Rodney." Sam swallowed as she looked at him.

He was pale when he looked back at her. "We're screwed."

"Can someone tell me what's going on?" Sheppard's voice on their transceivers reminded them he was still in the chair. "What's wrong?"

"Sabotage, that's what's wrong." McKay replied. "The city's operating system has been attacked by a Trojan Horse. There's code in here overriding the Ancient programming. Layers of it. This is going to take days, weeks to figure out."

"Okay. So, what does that mean?" Sheppard asked slowly. His tone indicated he already knew the answer.

"John, this is Carter. At least for now, we can't keep the system functioning without your help." She saw the time. He'd been keeping the lights, and everything else on, for more than four hours without a word. She mentally kicked herself for being so engrossed that she forgot him. "Oh, God, I'm sorry. We'll stop for a while."

"What?" McKay gaped at her. "We need to get working on this now."

"Rodney, I could use a few minutes."

"But, you've just been sitting there." McKay blurted before he could stop himself.

"Not really."

"John, can you give us some time to give everyone a heads up." Sam asked, deliberately watching code scroll across the screen in front of her.

"Yeah." They could hear relief in his voice.

"I'll let you know when we're ready. Thank you." She turned to the tech at the communications console. "Give me city wide, please."

The young woman toggled a control and nodded.

"Can I have your attention, please? This is Col. Carter. We need to shut down the Ancient systems ASAP. Department heads, let me know when you're ready."

She knew everyone in the city had been scrambling to prepare for another shut down. Plans for the possibility that the city might one day lose power were already in place. Emergency supplies were stored in strategic locations. Four hours was a luxurious amount of time, so nearly all preparations were completed already. Right now, they needed to be sure no-one would be in danger of injury when the lights went out again. The first of them checked in immediately. The last department gave the all clear at the six minute mark.

"Okay, John. We're ready."

xxxxxxxxxx

"Thanks." Sheppard was aching to move. He lifted his hands from the pads and opened his eyes. Four plus hours sitting in the Ancient chair left him stiffer than he would have thought possible. Could be the fact the damn chair was made from metal and some other weird, rock hard materials. He vaguely wondered if they did it on purpose to prevent anyone dozing off.

Ronon, listening to the brief exchange, grabbed the flashlights and stood up. Sitting around was not one of his strong points. He knew it wasn't one of Sheppard's either. He frowned when Sheppard merely leaned forward but didn't get up.

"You okay?"

"Yeah." John nodded then stood up. He grimaced as he stretched cramped muscles then adjusted the transceiver in his ear. "Col. Carter?"

"Yes, John."

"I'll be back in a few minutes."

"Take an hour. We need to compare notes, anyway. Just let us know when you're ready to start again."

"Will do." John said then turned the vox off on his radio and rolled his shoulders as he walked to the door. "Come on, let's get something to eat."

Ronon's stomach growled in agreement. "I was wondering when you'd get hungry."

xxxxxxxxxx

Col. Carter pushed back from the console and looked around at the personnel sitting at various consoles and finally settled on McKay. "What do you think?"

Everyone followed her gaze to the chief scientist, not daring speak up first. He didn't take long.

"We are screwed." He said it quietly, much more so than anyone expected.

"McKay." Sam said flatly.

He waved at the computer. "Beside the master operating system, it looks like every function vital to running and protecting Atlantis has a virus specifically written to attack that it. I found at least a dozen and there're probably more. We have to isolate and work on them individually."

"Where did it, they, come from?" Sam frowned at her laptop then at him. "When could they have been loaded onto the system?"

"It had to be recently. There was no evidence of viruses the last time a full sweep was done." He stopped and snapped his fingers several times. "We need to disconnect all Earth based computers from the city's system and scan them for viruses one by one."

"Yes, yes." Zelenka agreed. "There may be copies hidden on any one, or more, of them."

Sam nodded. "Okay, you two get your departments started on it. I'll make a city wide announcement, but we also need to set up search teams. Whoever planted the virus may have hidden a computer somewhere."

"It could be anywhere in the city." Zelenka frowned at the thought of searching the entire city.

"True, but we have to start somewhere."

"It's probably someone who went back to Earth last week. It'd be too much of a risk of being discovered to have a laptop sitting out there for too long." McKay pointed out.

"We can target the quarters and work areas of anyone who returned to Earth, but we'll start with anyone who went back in the last month." Sam looked at the two scientists. "Where would you hide a computer if you had to?"

xxxxxxxxxx

Sheppard stood in front of the weapons chair, scratching the stubble on his chin. He wasn't looking forward to sitting in it again, even for a few minutes. The impression he had earlier in the control room was more than reinforced in the first thirty minutes in the chair. The city was as close to dead as she could get without being destroyed. She couldn't talk to him and her silence made it extremely difficult. The dull ache that had been behind his eyes for days was worsening. Well, he thought to himself, at least the other shoe finally dropped.

He could feel Ronon watching him as he sat down, but the dim emergency lighting hid the Satedan's expression. "Look, you don't need to stick around."

"I've got nothing better to do." Ronon took up position in the chair again.

"Okay." It was no use arguing, so he turned his transceiver to vox. "Col. Carter, are you ready?"

"Yes, John. We're ready."

He shifted in a futile effort to make himself comfortable on the hard surface before placing his hands on the pads. A moment later, the city was alive again, at least to everyone else. It was going to be a long night.


	4. Chapter 4

**Chapter 4**

The familiar sound of an incoming wormhole caught them all by surprise. Chuck reached out to raise the shield then froze. "Col. Carter?"

There was no option. Sam just hoped that it activated and that Sheppard could control it. "Raise the shield."

McKay checked the IDC. "It's the Alpha site. They're early."

"What the hell's going on?" Sheppard demanded roughly.

"It's the check-in from the Alpha site, John." Sam replied quickly. "We'll make it fast. Are you okay?"

"Yeah." He grunted breathlessly.

"Atlantis, this is Maj. Owens. Sorry we're a couple of hours early. We're expecting a sizable thunderstorm shortly and didn't want to run the risk of lightening strikes." The apologetic commanding officer at the Alpha site half smiled on the screen.

The Gate at the Alpha site was exposed and the risk was very real, but Sam cringed at the thought of the strain this could be putting on Sheppard. "Major, this is Col. Carter. No problem about the early call, but I'm afraid this has to be brief. We have a virus in the operating system that is causing some problems. What's your status there?"

"Nothing to report, Colonel. We're in good shape." He was obviously concerned but didn't ask for further details. "Anything we can do?"

"Two things. You can suspend daily check in until further notice. Also, contact 621 and let them know the same. If either of you have an emergency, though, dial back in."

"Yes, Ma'am."

"The Apollo is due to be in orbit above Atlantis in a couple of hours. We'll let you know when we have everything sorted out here."

"Good luck, Colonel. Owens out."

The wormhole dissolved.

"John, this is Carter. Are you alright?"

It was a moment before he responded. It was more of a gasp than a word. "Yeah."

She winced. "It's time for a break, anyway. Can you give us a few more minutes to prepare?"

"Sure."

Sam turned to look at Rodney, who was quickly getting ready for the power down. There was no protest this time. The activation of the Gate startled them all, so he was certain it had been very hard for Sheppard to maintain the steady level of control without even a hint of an interruption.

xxxxxxxxxx

A pre-dawn glow was just beginning to lighten the sky when the Apollo emerged from hyperspace.

"Atlantis, this is the Apollo."

"Col. Ellis, it's good to hear from you." Even though she'd been kept informed of the ship's progress, Sam was happy the ship arrived. After the Alpha site dialed in a few hours before, she'd been uncertain about having John go back to the chair. They planned to be powered down at the scheduled dial in time, both to make sure it didn't overwhelm him and to see if the Gate would allow the incoming wormhole. Sam agreed reluctantly, but only when he insisted it did nothing more than startle him and he was able to continue.

"We'll be in orbit above you in twelve minutes. Our sensors indicate the city is back online. Can you confirm?"

"Col. Sheppard has been keeping the lights on so that we can determine the extent of the damage and start repairs. It looks like a Trojan Horse was loaded into the city's operating system. We have some scanner capabilities at the moment, but the whole system is so compromised it may be unreliable. We detected a pair of Hive ships on a course that could bring them fairly close to us. Can you keep an eye on them, please? We're sending you the coordinates."

"Be glad to. I'll have a report for you when I beam down."

"Thank you. We'll see you in a few minutes."

"Ellis out." He broke off communications.

"John, did you hear that?" Sam waited for him to respond.

"Yes, Colonel."

"I think we can stop. Can you give us the time until the Apollo arrives? We'll get you and Ronon beamed up once she's in orbit."

As promised, the Apollo assumed orbit within minutes. Department heads were again alerted that the shutdown would occur when the Apollo arrived so, as soon as Ellis radioed he was beaming down, Sheppard was given the all clear.

"Any time, John." Sam confirmed. The city went offline before she said his name.

Meager emergency lights were supplemented by the makeshift lighting set up the previous afternoon. The shadows cast by the harsh lights would soon shift and change with the coming sunlight. A deep sense of the vulnerability of the great city and its inhabitants made Col. Carter shiver.

xxxxxxxxxx

The conference room was full. Most department heads arrived on foot, some a little out of breath after climbing several flights of stairs. The Apollo obligingly beamed in anyone working in the more remote parts of the city at the same time as Sheppard and Ronon. The transporters were functioning while he was in the chair, but it was deemed too risky to use them except in the most extreme emergencies.

As a precaution, Col. Carter ordered that no Ancient technology could be used unless it was cleared with her or McKay first. Having the Apollo in orbit now would give them support for almost any emergency that might happen in the city.

Once they were settled, Sam looked at the expedition's quartermaster, Sgt. Williams. He was a small, wiry man, somewhere between forty and sixty years in age. An ability to do his job proven in two long tours of duty in the Middle East made him ideal to keep them fed.

"As you know, we have water. The plumbing seems to be in working order."

Rodney interrupted him. "For some unknown reason, the ventilation and plumbing systems, including hot water, are working. I guess it was overlooked while the viruses were being written."

"Yes, Sir. We have enough supplies on hand for two months, Colonel. We'll be taking a shipment from the Apollo, as well, that will give us another month, easily. Fresh fruit and vegetables will last for the next eight days, so after that it's canned and dried unless we can get to the sources we found on the mainland." The botanists quickly searched for and found several varieties of trees that bore edible, and tasty, fruit on the mainland not long after the city landed on the planet. Two root vegetables were also identified as edible and more were being tested. "There won't be much in the way of hot food until this is sorted out, but we've been there before. We've set up stations in strategic areas so that people don't have to get to the mess hall for meals."

"Thank you, Sergeant." Sam nodded her thanks and permission to leave. She could see he wanted to be out of there. Too much brass in the room.

"Thank you, Colonel." Williams stood and quickly left.

"Col. Ellis, were you able to contact the SGC?"

"Yes, through Midway. They asked if they should send help, but I let them know your concerns about using the Gate until more is known about what happened. General Landry said to let him know if they can do anything."

"Very good." She appreciated Landry's support, even if only in spirit at this time. "What about those Hive ships?"

"It's a fleet of two Hives and four cruisers, with a handful of minor support ships. The course they're on will take them a couple thousand light years away, but we're keeping an eye on them."

"Thank you. That's a lucky break for us." She looked to the CMO next. "Dr. Keller?"

"The infirmary is ready. It looks like all of the equipment there is virus free." Jennifer glanced down at a data tablet on the table in front of her. A state of readiness was the norm here. It was a way of life. "Thanks to the Apollo, we're fully restocked. As you know, we always have sufficient supplies to keep us going for six months if we were cut off from Earth. The only concerns I have are the blood products and some temperature sensitive drugs."

"Does that mean if we need blood…" McKay asked quickly.

"No, no." The doctor held up a hand. "We're fine for a while. The refrigeration units are well insulated and we have them connected to the naquadah generator assigned to the infirmary, so we should be fine. I just wanted to make you aware that we have perishable medical supplies."

"We have a couple of backup naquadah generators on the Apollo, and we can store anything you need." Ellis offered.

"I hope it won't come to that." Sam acknowledged. "Anything else, Doctor?"

Jennifer shook her head slowly. "Well, we have only one in-patient at the moment, but he's in good condition and should be discharged to quarters by tomorrow. Otherwise, it's been fairly quiet."

"Thank you." Next around the table was Lorne. "Major, how are the defense preparations coming?"

"Everything's pretty much in place, Colonel. Personnel are on readiness status, and all weapons and all equipment operational." He glanced a little uncertainly at Sheppard, wondering if the Colonel's sudden preoccupation with the city's defenses was merely a coincidence or something else. "I think we're as ready as we can be."

"Very good." She expected nothing less. Sheppard ran a fairly relaxed military setup here, but he kept his people well trained and prepared for whatever came their way. He led by example, and all too often by risking his own neck. They appreciated it and responded by giving their best. She turned to McKay. "Rodney, can you give us a brief overview of the situation, please?"

He looked up from his laptop. "Someone loaded a Trojan Horse into the operating system, and don't ask me when. Anyway, it released viruses targeting both vital and non-vital functions, including the main operating system, Gate operations, the shield, cloak, transporters, lights, etc. Actually, almost every Ancient function has been affected. And," he threw Sheppard a harsh glance, "as has been suggested, we can't just wipe the whole thing clean and load a back-up. We, meaning me, have to painstakingly go through billions, yes, billions, of code line by line…"

"McKay." John stopped him before he could get going. He wasn't in the mood.

"Do you have any idea how long this will take to fix?" Sam asked quickly. She could estimate it, but his far greater experience with the Atlantis computers would make the estimate much more accurate.

"Excuse me?" He stared at her for a second, opening his mouth to speak then stopping to swallow. "I don't know. As I said earlier, I need more time to determine the extent of the damage. That'll take at least another eight to twelve hours. We're disconnecting all Earth based computers except for those in Gate operations. There are hundreds of them, and they have to be scanned and cleaned of any viruses. We need to isolate the functions so that we can work on the programming and keep them from getting re-infected."

"Can you ballpark it?" Ellis asked with an even tone.

Rodney was already worked up, so any question from that particular colonel was not well taken. He didn't even try to keep the annoyance out of his voice. "Well, it depends on how much of the programming I will need to go around and clean up after the…"

John repeated the question a little more forcibly. "Rodney. How long?"

The astrophysicist turned to snap but saw his friend exhale wearily. He quickly factored in time spent without access. "It could be a week, maybe more."

"A week?" Teyla was appalled at the notion, as they all were. "So long?"

"You have to remember that we won't have 24 hour access."

Ellis rubbed the back of his neck. "That's a long time to be defenseless."

McKay bristled even more at the perceived slight. "This is unbelievably complex programming that's been corrupted by…"

"We know, Rodney." Sam said gently as she held up a hand to stop him. "We have at least one advantage, though. No-one knows this location."

"And Sheppard can fire the drones from the chair." Ronon spoke for the first time.

Sheppard rubbed the back of his neck. "Maybe."

"Are you considering evacuating non-essential personnel?" Ellis asked.

The leader of Atlantis shook her head. "Not yet. We have no indication that we are in immediate danger and the Wraith don't know our whereabouts. I hope we can get this resolved before we have to consider evacuation."

The question left unanswered for all of them was how an evacuation might be accomplished. The Stargate was seemingly out of the question, leaving only the Apollo. They all knew she wasn't capable of transporting the entire population at once.

"Well, the Apollo will remain here as long as necessary." Ellis said then his eyes narrowed. "What I want to know is, who did it and when?"

"It must've been the Trust. Who else would have the manpower to put something like this together and the ability to get someone to Atlantis to plant it? They have the entire operating system. Remember when Caldwell was taken over by a Goa'uld?" McKay stopped only long enough to breathe in. "Oh my God, there could be a Goa'uld here again!"

Col. Carter wanted to move the meeting on. They were all tired and there was far too much work ahead of them. "Everyone coming from Earth, either through the Gate or on the Apollo or Daedalus, is screened. All personnel at the SGC are checked as well. There are no Goa'uld here."

"I read the report about the incident." Ellis said. "The Trust is the most likely source, but could it have been that Wraith you had here?"

"No. The computers he had access to were isolated from the city, and I checked them out myself after he left." McKay answered then went on a little smugly. "The Trojan is too complex and would have taken a team of experts familiar with the all of the city's programming months of work to pull this off. It had to be the Trust. They probably started working on this when Atlantis didn't blow up last year."

Most of the table quickly glanced at Sheppard then away again. His part in that incident was still too close to the surface.

"He's right." Sam tried to move on. "If not, we have an enemy on Earth we don't know about yet."

There was a momentary silence around the table as everyone absorbed that frightening idea.

Teyla suddenly asked, "Rodney, did you not say that you need the system active to work on the coding?"

"Yes, that's right."

"I was thinking about that." Sam had been watching Sheppard, but couldn't tell if he was listening. He was sitting next to McKay and he was staring at the astrophysicist's laptop screen. It was easy to see he was tired, more so than the rest of them. "John?"

It took him a moment, but John finally realized his name had been said. "Sorry."

"We need to find you some relief."

McKay's head snapped around. "Don't look at me. I'm going to be a little busy fixing this mess."

"I'll be fine." Sheppard already knew it was unlikely that anyone else would be able activate the system.

"We have a lot of people up here working on the coding. You can't sit there 24 hours a day until this is over." Sam reminded him. There were varying degrees of effort needed to use and control the technology but she hoped someone could be found to relieve him. She glanced through the open doors and saw it was now a little brighter. They had all been up for more than a full day and needed to get some rest. Mistakes now could push an already dangerous situation beyond retrieval.

"You can't expect me to do both." McKay grumbled, feeling like he was being asked to do too much.

"Rodney, you and Maj. Lorne probably have as much chance of being able to relieve Col. Sheppard as anyone." Zelenka pointed out.

"If you have any luck, we'll round up some others that have shown they can use the Ancient technology with some ease and have them try it." Sam insisted. If these two couldn't do it, no one else would be able to.

"Yes, Ma'am." Lorne agreed, but he wasn't too hopeful. His own attempts to activate individual functions hadn't worked so far.

With an audible and annoyed sigh, McKay nodded. "Fine. Maybe I can take my laptop with me and work while I'm sitting there."

"The Apollo can beam you over to save time." Ellis offered. He knew the chair room was in another tower and it would be a waste of time and effort to get there on foot.

"Thank you, Colonel. We appreciate it." Sam smiled and nodded. "If you don't mind, let's see how McKay and the major do in the chair first."

"Sure." Ellis said as he stood up and activated his radio.

Sheppard remained seated as everyone else began to move. "Do we know if the Jumpers have been affected? We need to see if we can get them out of the bay."

"Excuse me?" Ellis asked.

"We should move at least a couple of the Jumpers out if we can. We may need them later." He didn't feel the need to elaborate.

Rodney snapped his fingers. "Of course. He's right. The Jumpers are vital if, well, something should go wrong."

"Okay, we'll do that now, too. We need to verify they're clean of viruses first." Sam agreed.

xxxxxxxxxx

The light from the Apollo's beam faded, leaving Sheppard, McKay, Lorne and Ronon standing near the weapons chair. The emergency lights were supplemented by a portable light brought in earlier by the Marines.

"We're here." McKay said into his mic as he waved Lorne to the chair. "Go ahead."

Lorne glanced at Sheppard, who cocked his head toward the chair in agreement. Evan compressed his lips and exhaled heavily. He crossed to the chair and sat down then hesitantly placed his hands on the pads. For a moment, they thought the chair would activate, but it only glowed weakly then darkened again.

"Come on. Concentrate." McKay urged, still annoyed at being there. More than a slight fear he might not succeed nagged at his ego.

"Rodney." Sheppard admonished him.

Lorne took a deep breath and closed his eyes, pushing back as if trying to coax the chair to move. It repeated the momentary glow but that was all. He tried one more time with the same results.

"Okay, enough already." Rodney snapped as he strode with false confidence to the chair. Lorne jumped up to let him sit down. "Like I said, I can't sit here and work on the code at the same time."

He placed his hands on the pads and leaned back. Rather, he tried to lean back. Nothing happened. He scowled at the pads then shifted as if to get more comfortable. With a deep breath, Rodney carefully lowered his hands on the ATA pads again. He got the same results.

"Col. Sheppard, how's it going?" Sam asked through their radios.

He tapped his transceiver to speak. "Maj. Lorne didn't have much luck. Rodney's trying now."

"Shhh!" Rodney squirmed then tightly screwed his eyes closed in an effort to concentrate harder.

John caught Ronon rolling his eyes and, with a shake of the head, warned him not to goad the astrophysicist. He waited a little longer as Rodney tried in vain to activate the chair. Finally, after watching his frustration grow with the futile efforts, John decided to stop him.

"McKay."

"Just…let me concentrate. I can do this." He didn't want to admit defeat, and tried to push into the chair even more.

Sheppard approached him and spoke quietly. "Rodney. Stop. Like you said, you can't be here and working on the programming at the same time. So it doesn't matter."

The argument worked and gave McKay an out. He groaned loudly and opened his eyes as stood up. "I'm glad someone realizes my efforts are more useful somewhere else. Can we go back now?"

"Not yet. We need to get the Jumpers out of the bay." Sheppard sat in the chair. "Col. Carter, are the pilots ready?"

"Yes, they are, and the Jumpers have powered up normally."

"Stand by." He placed his hands on the pads and leaned back.

McKay was both relieved and dismayed at the seeming ease Sheppard had with it. He mumbled under his breath, "That's so not fair."

"The Jumpers seem to be unaffected by the viruses, John." Sam informed him a couple of minutes later. "They're clear of the tower. The Apollo is going to beam you back up here. Ready?"

Sheppard sat forward then stood up. He barely glanced at the others. "We're ready."

They gathered in Col. Carter's office this time. She was already sitting at her desk when they materialized. The meeting would be very short. Her gaze moved from McKay to Lorne then to Sheppard. "Any luck?"

"No, but I wasn't given much of an opportunity." McKay blurted out, making a point of looking at no-one. The thought of not being able to activate the chair was aggravating.

"No, Ma'am." Lorne shook his head, glancing at Sheppard with concern. He pursed his lips in thought, something Sam caught.

"What is it, Evan?"

"There was something, only for a moment, but it's weird." He frowned deeply. "Normally, there's kind of a feedback when you use the Ancient technology."

"What do you mean?" She asked.

"Well, there's always something that tells you it's working." He searched for an example. "Like when firing a drone, I know where it is and what it's doing. More or less. It's hard to describe. The sensation is even stronger when flying a Jumper."

McKay snapped his fingers. "Yes, yes. He's right."

"What?" Ronon asked.

McKay held up his hands, momentarily at a loss for words. "The best way to describe it is it's like the Ancient technology that needs the gene is almost like a living machine. It's kind of like AI, artificial intelligence."

"Like the Replicators?" Lorne asked.

"No. Yes. Sort of, I suppose. You can feel it responding, know what it's doing. Now there's nothing. It's dead." He spun around to stare at Sheppard. "How the hell are you doing it?"

"Doing what?" Sam asked, trying to follow. She'd heard only vague descriptions about how people with the gene used it. She knew it was often a matter of simply turning equipment on or off, but interactive use was also needed from time to time. No-one had ever given her a satisfactory explanation on the latter. Even Gen. O'Neill avoided the question.

"Turning everything on, that's what." McKay cast an exasperated glance at her before looking at Sheppard again. "The city is dead. The virus is effectively preventing us from initializing the systems. How are you doing it?"

John wearily sat on one of the chairs in front of the desk. He thought for a moment before shrugging. "I don't know."

Rodney wasn't accepting the answer. "You don't know?"

"No, Rodney, I don't." Sheppard folded his arms. He didn't even want to try to explain it. The intensity in his voice stopped McKay's response before it started. "At least it works. Okay?"

"Yes, it works." Sam stood up, understanding he didn't need this discussion right now. "Right. I think we all need to get some sleep."

"No. No. No. We can't stop now." Rodney shook his head. "There's too much to do."

"Rodney. We can't afford to make any mistakes." She said. This was going to take a lot of time and they needed to pace themselves. "It's 0712. Get something to eat and as much sleep as you can. We'll start again at 1300."

When McKay hesitated, she stood firm. "I mean it. You can't do anything without Col. Sheppard, and he is going to obey a direct order, aren't you?"

"Absolutely." John started for the door. This was one order he was happy to obey.

"Fine." Rodney muttered petulantly. He watched the others leave, trying to decide whether he should at least attempt further argument. Realizing she was right in that Sheppard was necessary, he began to follow them.

"Rodney. Wait a minute." Sam said as he got to the door.

"Yes?" He turned back, surprised she'd changed her mind. When he saw her gaze was on John's back, he asked, "What…?"

"I want everyone to get some rest, particularly John." She walked around her desk and perched on the edge of it.

"Oh? You think Sheppard's more important than anyone else?"

"Rodney."

"Well, just because he can…"

"How difficult is it for John to activate the Ancient technology right now?" She asked pointedly, keeping her voice low to avoid any possibility of being overheard. If everything hinged on Sheppard's ability to give them access to the system, she needed to know what kind of effort he was putting into it.

He glanced at the door, beginning to understand her concern. "I honestly don't know how he's doing it at all. There's nothing there. It's as near to dead as it can be without unplugging the ZPM and naquadah generators."

"There isn't any way to work on the system without him in the chair, is there?"

He shook his head slowly. "No. The viruses are incredibly complex and have invaded just about every vital function and sub-routine. We wouldn't even be able to get to it."

"What about writing a worm?"

Rodney shrugged. "I was thinking about that. It may be possible, but I need to see more. Whoever did this knows his business. There're all kinds of safeguards against tampering written into the virus and there are probably multiple copies hiding everywhere."

"That's what I thought." Sam said with resignation, already knowing the answer to the next question but wanting confirmation. "How long do you think this will take?"

"Five days, if we're very lucky if we work twenty hours a day and throw everyone that's remotely competent at it. There's no way in the world Sheppard can keep…" He stopped, feeling miserable.

She released a long breath and stood up. "Well, the Apollo is here for as long as we need her. We'll just have to do the best we can. Okay?"

"Yeah." He turned to leave.

"Get some sleep." She reminded him.

"Not much else I can do." He replied, shoulders slumping as he walked out of her office.


	5. Chapter 5

**Chapter 5**

The few hours of sleep passed far too quickly for some and not fast enough for others. McKay found it difficult to sleep. His mind churned through what he'd seen in the programming. He knew Sam was right in that they all needed to be rested and clear-headed. He was also very aware that Sheppard would be stretched to the limit to keep the systems running while he, they, worked. The astrophysicist forced himself to relax. Power nap. He'd long used power naps during times of high pressure. A couple of hours and he'd be able to work twice as fast.

In his quarters, Sheppard had no trouble at all. As he took off the holster and sat down to remove his sneakers, he absently wondered how being mentally tired could feel more draining than physical weariness. Even the sunlight streaming through the windows didn't prevent him falling asleep the second he stretched out on the bed.

Five hours later, Ronon stood at the partially open door to Sheppard's quarters. Prying the doors open was relatively easy, but coaxing them closed again was quickly given up as a waste of time. The colonel hadn't even bothered to try. A MALP rolling by wouldn't have disturbed him.

"Sheppard." The Satedan's deep voice rumbled. He very briefly debated a more physical way to waken his friend, but dismissed it. He spoke louder. "John."

Sheppard's eyes blinked open and it took him a moment to orient himself.

"It's almost time."

John lifted his head to peer at Ronon then looked at his watch. His voice was thick with sleep. "Yeah. I'm awake. Give me a few minutes."

"Sure." Ronon leaned against the half open door.

"Sit down." John said as he rolled off the bed and headed to the bathroom. Protesting muscles made him grunt as he pulled off his shirt.

Ronon waited until he disappeared through the door before entering and dropping onto a chair.

True to his word, less than ten minutes later they were on their way. Sheppard was now dressed in his customary black BDUs and his hair was still wet from a quick shower.

"Col. Carter, this is Sheppard." He knew she and McKay were waiting to hear from him.

"This is Carter. What's your status, John?"

"Ronon and I are on our way to the mess hall for something to eat, then down to the chair room."

"Very good. I want to schedule fifteen minute breaks every two hours."

"What?" McKay interrupted. "Two hours?"

"Yes, Rodney." Sam replied firmly. "John, let me know when you're in position."

"Will do." He pressed his transceiver to deactivate the vox.

In the control room, Sam turned to McKay. "Rodney, every two hours."

He frowned at her, still not following. "Why? That's not enough time to get anything done. I don't need…"

"It's to give John a break, not you." She suppressed a groan. "He can't get up and walk away whenever he pleases."

Realization was slow. "I suppose, if we have to."

xxxxxxxxxx

The day passed in cycles of frantic activity punctuated by periods of anxious waiting for anyone involved in cleaning up the city's programming. It was only anxious waiting for everyone else. The need to let Sheppard get out of the chair every couple of hours was understandable but stressful. A solid fifteen minutes was used getting in then prepping to close down each time.

The military planning for the worst, and hoping it would never happen, joined in the search for the source of the viruses and patrolled. Civilian personnel not working on the problem at hand were pressed into the search as well. At Sheppard's insistence, it was mid morning of the next day before Sam called a halt. The last session had gone five hours straight, and three longer overall than she intended. They knew McKay reached a critical point in one area of the code so stopping would have meant redoing a large chunk of work.

She looked at the scientists around her. "Time to call it a night, well, morning, everyone."

Rodney exhaled noisily, not happy with the need to stop but acknowledging it was necessary. He turned to check that the others were ready for the power down then entered a few commands on his laptop. "Okay, we're ready."

Sam nodded and tapped her radio. "Col. Sheppard. You can power down now."

"Acknowledged." John responded. A moment later, the lights went out again.

Sam glanced at her watch and grimaced. They'd been at it for more than twenty hours. "Okay, folks. It's 1025 hours. We'll start again at 2000 hours."

"What? That's…" McKay started to complain but stopped at her look of warning.

It was a couple of seconds before anyone moved. Even though it was expected, the Ancient systems going offline was jarring. Slowly, everyone stood up and left, leaving Sam, Rodney and Radek to wait for the debriefing she wanted at the end of each day's work.

xxxxxxxxxx

Sheppard sat forward on the chair. He hunched over and pressed the heels of his hands onto each side of his forehead.

Ronon was already standing, waiting to beam out. He went closer. "You okay?"

"Yeah. It's just a headache. Sitting around all day isn't my idea of fun, and that chair is hard as a rock." He dropped his hands and slowly got up.

"Are you sure you're okay?"

"I'm fine. I just need to stretch my legs." John waved him off then adjusted his radio. "Apollo, this is Sheppard."

"This is Maj. Johnson, Colonel. Col. Ellis just beamed down. What can we do for you?"

"Can you give us a lift up to the Gate room, Major?"

"No problem, Sir. Now?"

"Whenever you're ready. Thanks."

"Glad to be of service, Sir."

xxxxxxxxxx

McKay paced the conference room, full of nervous energy that screamed the need to get back to work. He was not good at being on someone else's schedule, especially when the stakes were so high. Only the firm instruction from Sam to keep a lid on it prevented him exploding. He finally flopped into a chair.

Teyla, Zelenka, Lorne and Ellis were already sitting around the table. Each had a plate with sandwiches and fruit in front of them. The mess hall had been keeping the Gate room well fed and an enterprising cook's assistant jury-rigged electricity to keep a sizeable urn of coffee hot.

When Sheppard and Ronon entered, Rodney opened his mouth to speak but stopped when he saw his friend. Despite several hours of sleep, the colonel was not a good color. A laptop, plate of food and a half full coffee cup were arrayed in front of Rodney. Instead of speaking, he grabbed the cup and downed half of the hot liquid.

"Colonel, Ronon." Sam acknowledged their arrival. She pointed to the table of food. "The mess hall just sent up fresh coffee and sandwiches. Help yourselves before we start."

Ronon didn't need to be asked twice. He piled a plate high with food, and grabbed a bottle of water before sitting down. Sheppard picked up a single sandwich, an orange and two bottles of water. He drained one as soon as he eased into a chair.

When everyone was settled, Sam looked at Rodney. "Where are we at?"

He gulped a mouthful of food. "Mmm, I think we've found all of the affected areas of programming. I've started to rewrite code on the operating system. It doesn't appear the intent was to destroy the city. It's more like they wanted to disrupt only the access to anything that needs to be activated by the Ancient gene."

"And, to shut down the system." Zelenka added.

"Yes, well, I thought that was obvious." McKay retorted snidely. He looked around the table. "The viruses targeted individual operations, turned them off and blocked the ability to activate them again."

"How bad is it?" Lorne ventured. The glare he got from the chief scientist made him regret asking.

"It's disastrous." He cocked his head toward John. "If it weren't for our resident super user, we would be up the proverbial creek without any hope of finding a paddle."

They all turned to Sheppard, who was intent on the orange he was peeling. He noticed the silence after a moment and looked up. "What?"

"Haven't you been listening?" McKay demanded.

"Yes, Rodney. I can eat and listen to you at the same time." He replied evenly as he pulled the last of the peel off the fruit.

The astrophysicist frowned at John then cleared his throat before continuing. "Right. Very good. It's perfect timing, actually. Atlantis is on a new planet. The Wraith, and even the Genii don't know where we are. Disable our ability to use the Ancient technology and we may have to abandon the city. With the Gate bridge in operation, it leaves the place wide open to squatters.

"You would leave again?" Teyla asked, deeply troubled by the thought.

"No." John answered just before he popped a segment of orange into his mouth.

Sam shot him a side long glance. "It is possible we would be recalled to Earth if we couldn't resolve this. Only as a last resort, though."

"So, you'd destroy the city and leave the galaxy." Ronon's disappointment was obvious.

"No, it…" Sam stopped cold and looked at Rodney. "The self-destruct."

"Oh, my God." The color drained from his face. The others watched as he quickly typed on his ever present laptop. After several seconds, he threw his hands up. "I can't tell for certain, but it's unlikely the self destruct can be used. It's tied into the city's systems and would only work…"

They all turned their attention to Sheppard, who was chewing on another segment of orange. He swallowed. "If I'm in the chair. It won't come to that."

"No, it won't." Sam hurriedly agreed. She looked around the table, stopping at Ronon. "We aren't leaving if I have anything to say. And, at the moment, I don't see any reason to. Now that we know what we need to do it's just a matter of doing it as quickly and efficiently as we can."

"Yes, I'm working on the main operating system while everyone else…is working on minor functions and sub-routines." McKay said with a dismissive air. "And, after they're finished, I'll go through and correct their mistakes."

Sam quietly cleared her throat. "Yes, Rodney."

"If someone was planning to take over, how would they be able to fix the programming without Col. Sheppard?" Teyla asked.

"They must have figured out some way." Sam shook her head. It was a question puzzling her, too. "Given the resources the Trust seems to have, and the fact someone was able to get here to plant the viruses, they must have had something in mind. We're just speculating here. It could be the intention was for us to remove as much technology as possible on the Apollo and then just nuke the city. There are some factions on Earth that would like us to pull out of the Pegasus Galaxy completely and leave no way for the Wraith to get to Earth."

"What now?" Col. Ellis asked.

"We get back to work." McKay replied as if he were talking to a clueless teenager.

"But, not right now." Sam wondered if Rodney would ever get past the insult, but doubted it. There was too much work to be done and they'd barely scratched the surface. She glanced at John before ending the discussion. "Alright, we'll start again at 2000 hours."

"Let me know if you need anything, Colonel." Ellis said to Sam then tapped his transceiver. "Apollo, this is Ellis. I'm ready to beam."

Sam stopped John as everyone began to leave. "Can I have a word with you?"

"Sure. What's up?" He replied as he leaned against the table.

She studied his face. The work light in the room cast shadows that made it difficult to get a good look at him during the short meeting but she could now see the fatigue, and something else. "Are you alright? Do you need more time?"

John scratched the back of his head and dropped into a chair. "Nah, I'm fine. It's just a headache."

Sam's eyes narrowed as she tried to decide if he was being completely honest with her. She decided not, but there wasn't much she could do about it. "Rodney told me that by all rights, you shouldn't be able to initialize the city's technology."

"Well, he's wrong."

Curiosity overcame her reluctance to push further. "He and Evan said they couldn't feel anything, that it was more like trying to flip a dead light switch than what they normally feel. Is that what it's like?"

He looked away, frowning. The throbbing in his head was only marginally better for the food. Trying to answer this was not exactly what he wanted to be doing right now. He drew in a deep breath and blew it out again, hunting for a good analogy. "You're a pilot, right?"

"Yes." Sam replied slowly, wondering where this was going. She sat down again, too.

"Flying the city was like flying the biggest damn C-17 you can imagine." John realized she'd probably never flown a Globemaster. He massaged the right side of his forehead as he spoke. "When you're flying a jet or 302, you can feel the aircraft, right? You feel the aircraft, the speed, attitude, how well she's performing, if anything, anything at all, is out of kilter. You just feel it and know. Well, multiply that by about ten to the power of, oh, a thousand and you may come close to what it's like. When I was landing the city, I knew everything that was going on. I knew the altitude, the speed, how much power I was using. I knew how to use the minimum amount of power to land safely. It's really subtle, but the technology tells you. Don't ask me how."

It had been some time since she'd piloted a jet or 302, but Sam had a little better understanding of what he meant. There was nothing else that felt precisely the same. She tried to imagine that feeling on the scale of Atlantis. Then she tried to add the fact that Sheppard was sitting in a windowless room deep in the base of a tower, eyes closed, no gauges, readouts, HUDs or any other input normal to flying to let him know what was happening.

"Wow," was her only response.

"Right now, it's like I'm trying to do it blind, deaf and numb from the neck down."

Sam finally felt she had a small inkling of how difficult this was for him. Initializing and keeping the main operating system, minor systems, subroutines, even the lights, active and accessible for hours at a time had to be utterly exhausting. No-one could continue with just six or so hours of rest. "It looks to me like you need more than a few hours sleep. Do you want more time?"

"No, I'm fine." He said a little too quickly and looked away again.

She pushed. "An extra hour or two won't hurt, John."

"We're sitting ducks." He pushed back. "I'm fine."

"John."

"Look, I'll let you know if I need to stop. Okay?"

He was right. It was vital that the city be up and running as quickly as possible. Sam reluctantly agreed. "Okay, but I don't want you to hesitate."

"I won't. Thanks."

They stood up and began to walk out.

"John." Sam stopped him.

"Yeah?" He raised an eyebrow at her.

"Swing by the infirmary before you turn in." She saw his consternation. "Just to be on the safe side, I want Dr. Keller to check you out."

xxxxxxxxxx

The doctor sat on a tall stool at the monitor to study Sheppard's scan again. Something caught her eye during the test but her attention wavered when he moved and she turned to tell him to hold still. It was probably just a light reflecting off the screen, but Jennifer wanted to be certain.

The scan started at the top of his head and the flash she wanted to see happened in the first few seconds. It appeared to be evidence of abnormal activity but it faded quickly and was gone. She backed it up and watched again. It was definitely there.

Jennifer waited for image to make its way down his body and back to his head, closely watching for anything else. Nothing. There was nothing out of the ordinary. Whatever she'd seen on the first pass was gone on the second. She sat for a moment, thinking about what the tiny glow might have been.

She frowned at the device. Rodney likened it to a firewall, but, whatever the reason, the programming for the Ancient medical equipment was isolated from the rest of the city. She was grateful for that. Col. Sheppard needed to undergo the scan again as soon as he was available. If his accessing the systems was having an adverse affect on him, she needed to know. Just in case, Jennifer thought, it wouldn't hurt to run a diagnostic on the scanner. She typed the necessary commands and waited for the results.

xxxxxxxxxx

"Still got that headache?" Ronon asked John as they descended the stairs near the chair room.

The mess hall was keeping them and the Marines in the area supplied with food, coffee and water. Sheppard was moving a shade more slowly and spoke less each time he left the chair.

John tapped his radio to turn off the vox before answering. There was no sense in the others hearing idle chit-chat. He tore open a blister packet of Tylenol, threw the tablets into his mouth and washed them down with several gulps of water. "Yeah."

"Carter wouldn't mind if you stopped now." Ronon peered at his friend.

Sheppard checked his watch. "I'm okay. We've got only a couple more hours. Besides, I'd have to listen to McKay gripe. What's worse?"

Ronon thought for a second then nodded. He wasn't buying it for a second but knew arguing was useless. "You're right. McKay would be worse."

What John didn't want to say was that listening to Rodney waffle on for hours would be highly preferable right now. Telling Sam that this was like being deaf and blind and without any kind of sensation was true. It was nothingness. It was like being in deep water on a pitch black night. There were no reference points, no way of knowing where he was or what he was doing. He needed the chatter over his transceiver and Ronon's quiet movements to keep him from getting lost.

xxxxxxxxxx

"No. No. No. No. No!" Each word was louder than the last as McKay shot out of his chair. He swung around, glaring at the people around him. He was angry and made no effort to keep his voice down. "Who did that? Who the hell is messing with the primary operating system?"

"Rodney." Sam hissed at him. She turned off the vox on her radio.

There was silence while everyone either tried to shrink into nothingness or glanced furtively at those around them. McKay homed in on a technician who was hunched down and looking very miserable.

"You! Didn't I tell you to leave the operating system alone?"

"Yes, Sir. I was…I just…I'm…"

"Rodney." Sam said quietly, but with more urgency. Trying to stop him, she reached out to touch his arm.

He pulled away from her. "What was your assignment?"

"Transporters, Dr. McKay."

"McKay." She said as she stood up, trying to get his attention.

He fixed the young man with a look that could kill then turned to her. "Everyone here…"

"McKay." Sheppard's tone was quiet but it startled them.

Sam cringed as she activated the transceiver again. Up until now, the conversation had been sparse, quiet and welcome. "John, are you alright?"

"Yeah. Just tell Rodney not to shout." They could hear the strain.

McKay's anger instantly deflated. He said guiltily, "Of course. Yes. Sorry."

"John, we're going to shut down. Can you give us a minute?" Sam asked quietly.

"Is it time?" He asked.

"Yes. It is for today." Sam ignored Rodney's accusatory stare. They'd been working for more than fifteen hours and were tired. She knew most, if not everyone here, skipped sleep to hasten the work by studying back ups of the programming. That's what she'd been doing. Out of the last 72 hours, it was highly probable none of them slept more than ten hours in total. She just hoped Sheppard was getting more. Dr. Keller recommended he spend a maximum of twelve hours a day in the chair, and even that was pushing it. They'd already gone far over that recommendation.

xxxxxxxxxx

Ronon felt stiff and achy from the long hours of doing nothing more than sitting as quietly as possible. He told Col. Carter he would stay with Sheppard, babysitting she said with only a very small amount of humor. She realized Ronon might be better used somewhere else, but also knew that John wouldn't be able to order him around. The only other person she would want there was Teyla, who was in no condition to be that far from the infirmary under current circumstances.

The hardest part for the big Satedan was staying awake. Sitting still hour after hour in semi-darkness and relative quiet was very difficult for him. Between visits by the patrolling Marines, the only noise was occasional chatter from the control room and the quiet hum of the city when Sheppard was in the chair. After a while, Ronon realized that even the hum was…less than normal and a slightly different pitch.

Sheppard was almost completely motionless while he was in the chair. It often appeared to Ronon like he might be sleeping. Then he would watch closely and see his fingers move ever so slightly on the ATA pads or a muscle in his jaw jumping with tension.

Ronon knew Carter would be calling time in an hour or so, but it was hard to stay alert. The handheld electronic game Sheppard gave him held his attention for the first hour, but that was it. His eyes were getting heavy again.

"No. No. No. No. No!"

The Satedan was jolted out of his stupor by McKay's sudden outburst. He jumped up and crossed the room in two strides.

John screwed his eyes shut then blinked a couple of times, glancing at Ronon once. He was pale and breathing fast, trying to shake off the unexpected and loud disturbance without letting his control falter.

"You okay?" Ronon whispered.

"McKay." John said weakly as he looked at Ronon again and nodded then closed his eyes, took a deep breath and blew it out slowly. A moment later, he answered Sam. "Yeah. Just tell Rodney not to shout."

When Sam gave him the all-clear, John deactivated the chair but stayed in the chair. He was regretting the fact that he didn't listen to Ronon's suggestion to stop earlier. His brain felt like someone had stirred it with a spoon. Or a fork. Or something. It was like the time he'd gotten falling down drunk after a mission that, well, there was no use in bringing up a messy failure from so long ago.

John realized Ronon was waiting for him to move, but found the thought of standing up a little daunting. He'd spent the last three days connecting the city to its brain, but couldn't connect his own to his muscles.

When he didn't move, Ronon leaned down to look at his face. "Sheppard?"

He licked dry lips and tried to swallow. "Yeah."

"Col. Sheppard? Ronon?" Sam asked. "Is everything okay?"

Ronon decided everything was not alright. He adjusted his transceiver. "Col. Carter, I think…"

"Yeah, fine. Can we get a ride?" Sheppard interrupted, suspecting Ronon was going to say he should be in the infirmary. He knew he was going to be there soon enough, but wanted a minute to collect himself first.

"Sure. Stand by."


	6. Chapter 6

**Chapter 6**

One look at him told Sam that Sheppard was not fine. He was pale and drawn, and having difficulty with even the ambient light in control room. She was relieved they hadn't needed to turn the work lights on. The sunlight coming through the windows was muted by a thin cloud layer, but even that appeared to be painful for him. Sam spotted the glaring work light set up in the conference room and hurried the last couple of steps to turn it off. There would be sufficient light coming through the doors for the briefing.

"Hey! What'd you do that for?" McKay twisted in his chair and saw Sam nod toward the door. When he saw John, his mouth formed a silent "O". Guilt for his outburst bit at him again.

Sam looked around. "Okay, let's make this quick. I want everyone to get as much rest as possible before we resume at midnight."

"Midnight?" Rodney couldn't help himself.

"Yes. I think an extra couple hours of rest are needed." She looked at everyone but her gaze lingered on him in hopes of driving the point home.

She saw Ronon nod in agreement. He was essentially playing mother hen to Sheppard and knew what was going on with him. The friendship between him and Sheppard reminded her of O'Neill and Teal'c. There were differences, to be sure, but the underlying loyalty and trust was the same. It was a strong, even if unlikely, friendship.

The first thing that caught her eye when they entered was Ronon watching his friend very closely. Reading the Satedan was not easy, but Sam was certain she could see deep concern in his eyes. It wasn't difficult to understand. She wondered how long her 2IC would be able to keep the city online.

She turned to the chief scientist. "How are we doing, Rodney?"

He dragged his eyes away from Sheppard and cleared his throat. "If the dimwits we so laughingly call scientists and programmers would stop fooling around, we should need no more than fifty hours."

"Will any of the systems be available before then?" Teyla asked.

"No. Even though each affected function and subroutine have viruses targeted specifically at them, they are all tied to the main operating system. I may be able to get a few things running, but nothing will be stable until the operating system is repaired." He took a deep breath and continued the bad news. "By fifty hours, I mean it will take that long if we worked nonstop. Every time we power down, it takes time to reboot, retrace steps, etcetera. So, factoring in down time and the additional work, and testing, we're looking at something like four days, maybe four and a half, total."

That was a hell of a long time to remain so vulnerable. Everyone cringed inwardly then turned to Sheppard. He nodded wordlessly, but there was a look of uneasiness in his eyes that was hard to miss.

Sam asked Ellis. "Colonel, anything on the sensors?"

"We're keeping an eye on the Hive ships. We think they're headed for M5Q-491. If they maintain course and speed, they'll get there in three days. Do you know if it's inhabited?"

McKay and Zelenka were already working furiously on their laptops. Zelenka spoke first. "We have not visited it, but…"

"We've had intel that there's a working copper mine on the planet." McKay finished.

Teyla leaned forward, anxiety in her voice. "I know this planet. Approximately 4,000 people live there. We must warn them."

"I know and we will." Sam agreed.

"Can they hide in the mine?" McKay asked.

Teyla shook her head. "No. The mine entrance is very close to the town and quite obvious. The Wraith will find it immediately."

"We can't use the Gate, can we?" Ellis asked.

"No." Sam answered, flicking a glance at John.

Even though she knew it wouldn't work, Teyla suggested, "Is there anyway to contact the Alpha site or M6P-721 by radio? They would be able to use the Stargate to warn the people of that planet."

"No. They don't have a sub-space radio." Rodney answered with frustration. "That needs to be rectified. We can't keep relying on the Gate to contact them. It's ridiculous."

"Yes, Rodney. We know and the SGC is working on portable units we can deploy in the field." Sam said.

Ellis asked, "When are they due to check in again?"

"The Alpha site dialed in the first day. We asked them not to dial in again unless there's an emergency, and to let 721 know as well." Sam replied. She was almost regretting the order, but her biggest worry had been Sheppard. They knew the incoming wormhole added a huge amount of strain. "We didn't know what it would affect here."

"We can use the Gate." Sheppard said quietly.

Sam shook her head. "I don't know, John."

He waved one hand. "Look, it won't take long to send a couple of squads through to the Alpha site in a Jumper. They can cloak and go to 491 from there. If everything's okay, they can warn the population, help them evacuate then head back to the Alpha site."

"We may not even be able to dial the Gate." She was not liking this idea at all. Holding the operating system and various functions they working on active was one thing. To add dialing the Gate and keeping the wormhole open was something else entirely.

He persisted, looking her in the eye. "We won't know until we try it."

"The Apollo could be there and back in about sixteen hours." Ellis offered.

Zelenka squinted at his laptop screen then looked up. "Uh. There is also the option of the Apollo going to M2R-914. They can use the Gate there to get to 491 and the round trip is only seven hours."

McKay was appalled at the notion. "What, and leave the city completely open to attack?"

Sam considered the ideas for several seconds. They needed to get word to 491, but couldn't leave Atlantis vulnerable for even seven hours. It wasn't the threat from space as much as through the Stargate. Even though she didn't want to, she agreed with Sheppard. "John, we'll try your way first. We can send the away team to the Alpha site and they can update Maj. Owens on our situation at the same time."

"Okay." He nodded and stood up.

"It'll take a little while to prepare an away team. In the meantime, I want you to see Dr. Keller."

xxxxxxxxxx

Sheppard was halfway down the stairs, heading for the infirmary, when someone rushed up behind him. He glanced back to see McKay hurrying to catch up. He stopped and turned around.

"Rodney?" He was surprised to see his friend away from the computers and hoped he wasn't going to get an earful about getting back to work.

"Sheppard. Uh…Um...Well." Rodney suddenly didn't seem to know what to say.

McKay being at a loss for words was something else John wasn't expecting. "What's up?"

"Well, apart from the distinct probability that we will need to blow up the city and leave Pegasus…" Rodney cleared his throat. "I, uh, just wanted to ask how it's going."

John thought for a moment. "I'm the one just sitting in the dark. I should be asking you. Can this be fixed?"

"Yes." He answered with his typical McKay confidence then faltered. "Well, I think so. If I had ten days and few people that had half a clue, I might be able to get it done."

John knew the time constraint was mostly on his own shoulders. "Is there any way to fix the connection so that Lorne or someone else can sit in the chair? You'd have the systems available 24 hours a day."

"I wish." He sighed heavily. "We have just one little problem. There is no one thing in the programming that specifically addresses the gene for the entire system. I'm afraid that for the present catastrophe, it's all, meaning you, or nothing."

"Okay." John said slowly. It was just confirmation of what he already knew. "I'll try to convince Dr. Keller and Col. Carter to let me stay longer."

"Thanks." Rodney said thoughtfully. He turned to go back to the control room then stopped, to watch John start down another flight of stairs. "Wait. Are you going to be okay?"

"Sure." He was as reassuring as he could be, even though they both knew it was probably a lie.

xxxxxxxxxx

Col. Carter stood in the door, frowning at prone figure on the bed. The only light in the room was provided by a small lamp, so Sam couldn't tell if Sheppard was awake.

Jennifer quietly guided her to the next room, casting a quick glance back at him, she whispered, "He's asleep."

They talked in hushed tones. "How is he doing?"

"I'd like him to sleep for as long as he can." Jennifer took a deep breath. "John has a migraine, or something like a migraine. I'm guessing it's severe, but he's refusing to let me give him anything for it. He doesn't want to risk any of the side effects."

"Side effects?"

"Drowsiness, dizziness, and nausea, which he already has. He's afraid he won't be able to concentrate."

"How long will it last?"

"It's hard to say. Without some kind of assistance, a migraine can last for days." She paused, lips compressed. "This isn't a classic migraine, though, so I have no idea."

"Damn." Sam folded her arms. There wasn't enough time. They needed to know now if the Apollo would have to make the journey to 491. She wasn't about to let a settlement of that, or any size, fall prey to the Wraith.

"Why?" Jennifer asked.

"We believe a Wraith fleet is headed for a large settlement on a mining planet. Ordinarily, we'd just send a team through the Gate to evacuate the inhabitants." Sam explained.

"The Stargate can't work without Col. Sheppard, can it?" Jennifer finished.

"No." Sam compressed her lips. "It may not work anyway, but John wants to try to it. Otherwise, we'll send the Apollo to the nearest planet with a Gate to send an away team."

"How long will that take?"

"Seven hours for the round trip."

Jennifer fidgeted with the tablet. "We'd be vulnerable, wouldn't we?"

"Is the away team ready?" His sleep roughened voice made both women jump.

"John." Sam glanced from him to the young doctor. "Yes, they're ready."

He gave Jennifer a look that said she shouldn't argue. She sighed in resignation. "Okay, but I want you back here as soon as you're done."

"It won't take long." He said as he carefully replaced his transceiver. "Apollo, this is Sheppard. I'm ready."

As the beaming light faded, Jennifer looked at Sam. "I mean it. I want him back here as soon as possible."

"I'll have Col. Ellis beam him back." Sam agreed.

The doctor chewed her lip as the colonel asked to be beamed back to the control room and then disappeared. She turned to see Dr. Reynolds approaching from the other direction.

"How is Col. Sheppard?" Beth asked as they walked through the infirmary to the scanner.

"Okay, for now." Jennifer pulled up his latest scan. "Take a look at this."

Beth looked over her shoulder and whistled softly. "Wow. What's the magnitude of the increase?"

Jennifer typed a command on the keyboard, showing the psychologist several scans and statistical results. "Rodney believes this virus thing is going to take several more days of very intensive work to fix."

Both women watched the image. Beth looked at her young colleague. "Have you run an extrapolation?"

"Yes. I don't think he should be in the chair for more than twelve hours a day, but I know it'll be more like fifteen to eighteen. So…" She pressed a couple of keys. "This is over four more days at an average of sixteen hours."

The image morphed, the area of activity enlarging then shrinking then enlarging again. After the first day, there was too much of an increase for it to return to normal. The area of increased activity grew with each passing day.

Beth whistled again. "I can see why you're worried. How is John holding up?"

"As well as you might expect." She turned the device off. "What worries me is that he'll keep this up until it kills him."

"Me, too."

xxxxxxxxxx

Sheppard watched as Ronon coalesced just outside the chair room door. He didn't bother to protest the obvious babysitting duties of his friend. Instead, he sat on the chair.

"Col. Carter, I'm ready."

"Alright, John. Go ahead." She responded.

He took a deep breath, sat back and placed his hands on the pads. The chair activated and the city came to life again. Seconds passed, then a minute then two.

McKay's frustrated voice came over their comms. "It's not going to work. You can shut it down."

"What's wrong?" Sheppard asked.

Sam answered him. "The DHD won't lock, John. We'll figure out something else."

xxxxxxxxxx

"Wait. Hold on."

Sam and Rodney looked at each other, wondering what he could possibly do. Opening a wormhole had been a long shot at best.

"Try it again." He was barely audible.

McKay's hand hesitated for a second before he pressed the first symbol for the Alpha site. When it encoded, he quickly completed the sequence. The wormhole formed with a highly satisfying kawhoosh.

"Maj. Owens, this is Col. Carter. Do you copy?"

"This is Owens. Good to see you've fixed the problem, Colonel." The Major replied.

"We actually haven't, Major. There's no time now to explain." Sam watched a Jumper descend into the area in front of the Gate. "Capt. Hillman is coming through with an away team in a Jumper. He'll fill you in."

"We're clear of the Gate, Colonel."

"You have a go, Captain." Sam said. The Jumper quickly pivoted and disappeared through the event horizon. It was packed with a dozen Marines and their equipment, the minimum she thought necessary for the mission.

"They've arrived, Colonel." Owens said within a few of seconds.

"Thank you. Major, we'll dial back as soon as we can."

"Copy that, Colonel. Good luck." Owens replied.

McKay hit the command to disconnect the wormhole and it disappeared instantly. The whole process had taken less than two minutes.

"John, you can shut it down. Thank you." Sam said as the puddle dissolved. Everything powered down before she finished speaking.

xxxxxxxxxx

Ronon watched Sheppard while he listened to the exchange. When the first attempt at dialing out failed, Sheppard opened his eyes and stared at some distant thing. He worked to slow his breathing and concentrate on making the Gate available for dialing. Ronon could only guess at what he was going on.

"Wait. Hold on." John took a couple of deep breaths then closed his eyes again and whispered, "Try it again."

They both heard sound of the Gate activating and the hurried discussion between Col. Carter and Owens over their transceivers. Ronon could see the muscles in Sheppard's jaw tensing as the seconds ticked by at a snail's pace. Finally, the all clear was given and he shut everything down again.

John leaned forward and pulled the transceiver from his left ear. He pressed his fingers around each temple and just sat there. Even though the sound from the control room was muted, it made the nausea he felt worse. Right now, John wanted to be somewhere dark and silent. Then he realized, no, that's where I've been.

"Sheppard?"

He looked up slowly. The pounding in head seemed to increase exponentially with the movement. He carefully stood up, keeping one hand on the chair to steady himself. "Yeah."

Ronon grabbed his arm. "Apollo, this is Ronon. We're ready."

xxxxxxxxxx

Dr. Keller ordered that the area of the infirmary where Sheppard would be was quiet and dark. It was as close to the scanner as possible. She wanted to make sure no damage was being done by his time in the chair. She arranged for the Apollo deposit him in the room and that everyone else was out of the way. Only she, Alex and Marie, two of her best nurses, would be there. All would be done quietly and with the minimum of fuss.

As the sparkling light from the beam disappeared, she could see Ronon needed to support him. John was pale and kept his head down, one hand shielding his eyes. Ronon relaxed his grip slightly when Alex stepped up to take his other arm.

"John, I want to run a scan, if you don't mind." Jennifer said softly. She was both deeply concerned and very curious about what she'd seen earlier. To her surprise, after only a moment's hesitation, he merely inclined his head a fraction in agreement. She pointed toward the scanner room. "I promise to make it fast so you can get some rest."

John scowled at Ronon and Alex, waving them off as they tried to help him onto the table. He lay down and closed his eyes.

Jennifer turned to the controls and powered up the machine, not noticing Ronon following to watch the monitor over her shoulder. The image showed what she suspected, only now the area of heightened activity was significantly larger and brighter. She adjusted the control so that the scanner remained over his head. This level of activity was not normal for Sheppard, or anyone else. After studying the image for almost a full minute, Jennifer leaned closer, her mouth forming an "O". The readings indicated it was very slowly diminishing.

"Doc?" Ronon's deep voice was a low rumble.

"Yes. Yes, of course." Taking one last look at the screen, she turned the device off. "Okay, let's get you to bed."

He frowned at Jennifer as Alex guided him to a nearby room. "I can sleep in my quarters."

Yes, I know, but you can hardly stand on your own right now. You'll stay here, where I can keep an eye on you." Jennifer spoke quietly but firmly. One look at his color reinforced her decision to keep him in the infirmary. He was white as a sheet and the pain was etched on his face. "Come on."

He said nothing as he watched the nurse gently pry the forgotten transceiver from his hand. His brain wanted to stop working and everything was becoming distant and fuzzy.

"Look, I'm willing to let you try to get through this without medication, but I insist that you stay here."

"Kay." He finally agreed. Walking without assistance was iffy at best, and the nurse had already removed his sidearm and was unbuttoning his shirt.

"Good." She turned to Ronon. "Alex can handle this. Why don't you get something to eat and some rest yourself?"

He looked from her to Sheppard and back again. She raised her eyebrows and pointed to the door. "He needs to sleep. Don't worry, we'll take very good care of him."


	7. Chapter 7

**Chapter 7**

"Dr. Keller?" Sam stood at her office door. "Sorry it took me so long."

"No problem, Colonel. It gave me some time to go over the results." Jennifer indicated a vacate chair. "Please."

Sam accepted the offer. "Is there a problem? Is John alright?"

"That's what I wanted to see you about. He still won't let me give him anything to help the migraine, but he is sleeping."

"Can he keep doing this?"

"I don't know, but I doubt that he'll be able to continue for much longer at the pace he's been going. The headache is much worse." She stopped and chewed her lip for a moment then swiveled the laptop on her desk so that Sam could see it. "But, that's not all of it."

Jennifer tapped a key on the laptop and an image of Sheppard's baseline scan showing the brain appeared. She moved the cursor. "This is a scan of Col. Sheppard that I ran during his physical three months ago. It's consistent with prior scans."

Sam looked at her. "I don't understand."

"I wanted you to see the difference." She pressed another key. "This is the scan I took a few days ago, before all this happened. See these areas?"

The colonel squinted at the screen. "I'm not sure."

Jennifer manipulated the image, overlaying the second on the first then moved the cursor over a couple of areas. "There is evidence of activity that doesn't seem to be normal."

"Could it just be that it doesn't show up all the time?"

She compressed her lips and shook her head then pulled up another scan. "No, I don't think so. This is the first one taken after all the systems went offline. As you can see, there is a little more synaptic activity." She added a third image then a fourth image. "This was yesterday, and three hours ago."

The dramatic difference between the images made Sam blink and lean in closer. She turned to the doctor. "What is that?"

"To be honest, I'm not sure. The scans indicate use of more of the brain than is normal, for anyone. It may be the level of concentration necessary to activate the systems requires it, and the interaction of someone with the Ancient gene to the technology facilitates it." Jennifer shrugged. "I have no proof, of course."

"This looks a little like the scan you did on Davos." Sam looked back at the screen and thought about what happened to Gen. O'Neill when the Ancient library was downloaded into his brain. "Is…is this permanent?"

"It is similar to Davos' scan, to a very limited degree, as well as to what happened to Rodney when he accidentally triggered the Ancient ascension device. I'm not certain, but I don't think it's permanent. This scan is from earlier today." Jennifer closed the other images and started a video. She pointed to different areas of the picture. "It shows the activity is diminishing."

"I'm not sure I see it." Sam stared at the screen.

"It is, slowly." The doctor paused. "I think that if I had been able to run the scans as quickly as I did today, the others would show something similar. It may just be his brain is taking time to recover, so to speak, and evidence of the extraordinary activity to disappear."

Sam sat back, blowing out a long breath. This was different. "Does this happen whenever John, or anyone else, uses the Ancient technology?"

"No, not that I know of." Jennifer thought for a moment. "It would have been interesting to check him after he landed the city. That must have taken tremendous focus and control."

"Yes." Sam agreed. That not so small feat still amazed her. She suddenly asked, "Is this causing any harm?"

"Apart from the migraine, for want of a better diagnosis, I don't know. This is all new territory."

"Can he continue?" she asked again.

"That depends on the colonel. Right now, I'm going to let him sleep for as long as he can. I want to take as few chances as possible until I know more about the affects this is having on him." She shrugged apologetically. "Sorry."

Sam offered her a reassuring smile. "Don't apologize. We need to keep a close eye on this."

xxxxxxxxxx

Col. Carter sat back in her chair, staring at the top of her desk as she pondered the delay forced by Dr. Keller's insistence that they let John sleep. The lab was processing the latest blood work, but would not have the results for at least another hour or so. The sample from the day before showed an elevated level of the protein produced by the Ancient gene, but it wasn't a stretch to attribute it to the hours of effort he was putting in. The scans showing the unusual brain activity were, however, both troubling and intriguing.

She wholeheartedly agreed with the doctor. John was exhausted before they needed to open a wormhole to send the away team to 491. Right now, she was worried about letting him continue at all. There had to be a way around needing to use him for such extended periods of time.

"Sam?" McKay interrupted her thoughts.

She looked up. "Sorry. You were saying?"

"I asked what Keller said about Sheppard." Rodney was hoping for the extra time he wanted.

"Dr. Keller is adamant John doesn't use the chair for more than a few hours at a time. The effects are…"

"I thought she didn't have the test results back yet. It can't be that bad, can it?" He asked a little impatiently.

"Rodney. It's affecting him a lot more than he's letting on." She decided not to tell him about the scans. There was nothing to be gained until they knew more.

"What do you mean?" His brow pulled down in thought then he suddenly became alarmed. "It can't be more than a headache, can it? Is there a problem using the Ancient technology? I use it all the time. Are there side effects I don't know about?"

"No, Rodney. We don't know of any problems with normal usage." Sam needed to take a deep breath and reminded herself, McKay was himself exhausted. They all were. She doubted he understood. "It's that John has been keeping the entire city working by sheer will power alone."

"He can do this stuff in his sleep." He shook his head, but his dismissal of her comment was half-hearted, and probably more to convince himself than anyone else.

"You couldn't make it work at all, so it must be extremely stressful for the colonel." Radek reminded him.

"I could have. I just wasn't given enough time." He was indignant. "Besides, I can't do that and fix the programming. Despite what many people might think, I'm not Superman."

Zelenka's eyebrows went up ever so slightly. "No, Rodney. No-one thinks that."

"The point is," Sam brought them back to the topic at hand, "that this will take more time than we hoped. It's too risky for John to continue putting in more than twelve hours a day. You know it was very difficult for him to give us the Gate earlier."

He finally conceded her point, and exhaling noisily, said, "Alright, but this is going to take at least another day if we cut back the hours working on it."

xxxxxxxxxx

Sheppard woke slowly, taking some time to remember why he felt like crap. Even before opening his eyes everything was blurry. Sounds, sense of touch, everything, seemed muffled. There was an improvement from earlier, he thought to himself as he lifted his left arm to check his watch. Gone. Why do they do that? Why do they always take the watch? He carefully looked left then right for the bedside table, trying to move his head as little and as slowly as possible. The blurriness was getting better and the headache had eased somewhat, even though it still felt like his head was in a vice. It was a relief, though he might have thought that too soon. He had to try standing up first. He carefully pushed himself to a sitting position and swung his legs off the side of the bed.

"Colonel?" Dr. Keller was standing in the doorway. When she saw he was awake and intended to get up, she rushed in. "Wait. Wait."

"I'm good." He rubbed his face with both hands then blinked at her, trying to clear his vision. "What time is it? Where's my watch?"

"About five a.m." She'd let him sleep more than fifteen hours but he was still pale and unsteady. "And your watch is right here."

She kept a close eye on him as she opened the drawer in the bedside cabinet and pulled it out. He peered at it for a couple of seconds before giving up trying to focus and put it on.

"Damn it. Why didn't someone wake me up earlier?"

"Because I'm the doctor and I said not to." Jennifer smiled pleasantly at him then became serious again. "How are you feeling?"

It was tempting to lie, but John figured he probably looked like death warmed over. "Better."

"Define better." She stood in front of him to keep him from getting up.

"Aw, come on." John wasn't in the mood for this. When she didn't move, he sighed, "The headache is a lot better."

"The nausea?"

"Pretty much gone." It was actually the truth. The headache had gone from blinding, non-stop pain to tolerable, and his stomach was growling. "I'm hungry."

"That's good. I want you to get something to eat, but nothing heavy." Jennifer smiled and took a step back.

John was slightly suspicious of how quickly she relented, and decided to get out before she changed her mind. He dropped off the bed, but the sudden movement made his dizzy for a moment. Jennifer, expecting it, reached out to steady him.

"Take it easy."

"Okay, okay. I'm good." He mumbled irritably.

He didn't see her expression soften. "I know, but I want to run another scan on you. If it's clear, I'll let you go."

Twenty minutes later, Jennifer watched him leave. She'd run the scan, collected blood and urine samples, gave him more Tylenol and reluctantly sent him on his way. The scan showed her what she expected after so many hours, brain activity that was closer to normal.

While he was asleep, Jennifer asked Sam to have him beamed directly to the infirmary after each day's work. Tracking the changes was important for at least two reasons. First and foremost was concern for John's health. The second was that this was the only time anyone from the Milky Way was known to have this kind of synaptic activity without use of brain boosting Ancient technology. And, the only known human in Pegasus was Davos.

Jennifer emphasized that he should be in the chair a maximum of twelve in every 24 hours. She had a strong suspicion that he barely got the away team through the Gate. There was a very real danger of him losing control in the middle of a crucial piece of work. Even Dr. McKay would have to admit that could be disastrous and had to be avoided.

xxxxxxxxxx

"I know you must be very tired of sitting and doing nothing, Ronon." Teyla studied her friend's face when he said nothing. There was something in his eyes that disturbed her, but she couldn't tell what it was. She checked to make sure that the mess tables nearby were empty. "What is wrong?"

"I don't..." He shook his head sharply, but stopped and stared at the door.

She looked around to see Sheppard approaching the table. Smiling, she asked, "John, how are you?"

"Hungry." He answered as he put his tray on the table and sat down. She was pleased to see his appetite was good. He took a large bite out of a sandwich and looked her up and down. "You?"

"I am very well, thank you." She inclined her head. She wanted to repeat her question, but knew he wouldn't elaborate.

He was a little suspicious. "What are you doing up at this hour? Shouldn't you be getting more sleep?"

"I am getting plenty of sleep." She rolled her eyes towards Ronon. "I just mentioned that I would be happy to take Ronon's place for a few hours."

Sheppard frowned at her and set down his sandwich. "No. I actually don't need anyone there, despite what everyone seems to think."

"Sitting quietly would not pose a problem for me." Teyla shrugged with a resigned smile. "Dr. Keller only said that I should not be on my feet so much."

"I don't need a babysitter." He picked up his sandwich again.

"I'm not babysitting you." Ronon growled. "Carter asked me…"

He trailed off when Sheppard took another bite of food with an air of disgust.

"I am sure it is not babysitting, as you say." Teyla said gently. "Col. Carter is only concerned for your welfare, as we all are."

He swallowed and drank a mouthful of water. "I have a radio and there are a couple of squads of Marines patrolling the area. If everyone's so worried, they can swing by the chair room more often." He saw they were not convinced. "Look, buddy, I'm just saying there's nothing to do. The Apollo can beam me out any time I need it. It's just a waste of time."

Ronon folded his arms over his chest and leaned back in his chair. "I've got nothing better to do."

"You can help with the defenses."

"Lorne's got it under control."

Sheppard groaned and put the rest of his sandwich in his mouth.

xxxxxxxxxx

"Well, it's about time." McKay huffed when he saw Sheppard climbing the stairs to the operations area with Ronon.

"Sorry I'm late. For some reason, my alarm clock didn't work." He cocked his head sideways, aiming the apology at Sam and more or less ignoring Rodney. The combination of emergency lights and bright work lights cast strange shadows around the entire space but he could see Zelenka, as well as several other people, sitting at computers and laptops, ready to work. He assumed the doctor must have let them know he was up. The few minutes he took to get to his quarters, shower then grab a bite to eat gave them time to get to their stations.

Sam half smiled at him. "Don't worry about it. We all needed some rest. How are you?"

"I'm good. Everyone ready?"

"No, we just like sitting around at dawn, doing nothing!" Rodney snapped. "Can we get on with it?"

John adjusted his radio. "Apollo, this is Sheppard. Can you beam me to the chair room, please?

They were waiting for him, too. A split second later, he and Ronon stood in from of the chair. John was resigned to having someone hovering, but still didn't like it. Without a word, he turned and sat down.

xxxxxxxxxx

Fingers tapped anxiously on the keyboards of laptops all around the operations area. Rodney alternately folded his arms and sighed, tapped like everyone else or huffed impatiently. As soon as the systems came up, they all began working as one. A kind of rhythm had developed during the last few days. It was a frantic, desperate rhythm, but it was moving them forward. Even the chief scientist was considerably quieter than normal. They needed just a little more time. A couple more days and this would be behind them.

"Dr. McKay? Col. Carter?" Zelenka sat back then leaned close to his laptop screen, a deep frown causing his glasses to slide down his nose. "I think we have a problem."

"Problem?" They said in unison as they swiveled their chairs to look at him. McKay went further. "What kind of problem?"

"Oh, no." The Czech started typing as fast as he could.

Sam and Rodney turned back to their computers. McKay asked, "What is it?"

"It's the…the…" Zelenka did not stop his furious typing and did not look up.

"Crap!" McKay choked out as he hunched forward. He opened his mouth to shout at him then remembered Sheppard, so he hissed. "What did you do?"

"Nothing." Radek replied, continuing to pound keys as fast as he could. "I was verifying code when it suddenly started to rewrite on its own."

Sam saw what he was working on and looked at the people working around them. "Everyone stop work. Now."

A dozen pairs of hands rose from keyboards immediately. Then a dozen pairs of eyes peered from one screen to another, trying to see what was happening. Sam swiveled back to her computer and started working.

Forty minutes later, the three of them hesitantly slowed to a stop.

"What happened?" Chuck asked. His station next to the colonel allowed him to follow some of it.

"Six hours worth of work down the drain, that's what happened!" McKay was livid. "Somewhere in the city, there is a computer some idiot forgot to unplug, and it has at least one of the viruses."

"Or, it was left just for this purpose." Sam added with deep anger in her voice. She picked up a handheld radio. "Maj. Lorne, this is Carter."

"This is Lorne, Colonel." The response was immediate.

"Did you hear?"

"Yes, Ma'am."

"We're certain there's at least one computer out there we have to find. Second every able bodied person you can find. I'll ask Col. Ellis if he can spare any more personnel to assist in the search."

"Thank you, Colonel. That'd be a big help. We'll find it."

"Thank you, Major. Keep me informed." She knew that all search parties had three members, including a Marine. Many of them were too far from operations to get back quickly without the Apollo's beaming technology, and there were more than seventy teams out there. The city was huge, and the frantic search for the proverbial needle was aggravatingly slow. They needed as many people the Apollo could send.


	8. Chapter 8

**Chapter 8**

"Colonel?"

Ellis turned and walked to the young woman standing at the Apollo's long range scanner. "What is it, Lieutenant?"

"The Wraith fleet we've been tracking has just jumped into hyperspace again and they've changed course, Sir."

"Where're they headed?"

"Here, Sir. Atlantis." She manipulated the scanner's controls and a dotted line appeared, tracking in a straight line from the enemy ships to Atlantis. The colonel felt a cold knot in his stomach. The couple of days spent sitting in orbit while the frantic work in the city below continued was long past being tedious. The ship's crew was accustomed to inactivity because of the trips between galaxies, but this was grinding. Other than searching for errant computers, they really couldn't even help the personnel in the city. This, however, was not the activity anyone would have wished for.

"ETA?"

"At present speed and course, Sir, thirty hours."

"Damn." He muttered as he watched the blip on the screen for several seconds then turned to another crewmember. "Beam me down."

"Col. Ellis?" Sam looked up from her computer when Ellis appeared. His expression was dark and the fact that they were still more than an hour from the scheduled shut down gave her a sudden sense of foreboding. "What's up?"

He glanced around at the number of people working at various computers in the area. Reluctant to make a general announcement to everyone in earshot, he got closer. "The Wraith fleet we were tracking has changed course."

McKay stopped to listen. He couldn't help asking, "Where are they going now?"

"As far as we can tell, here." Ellis dropped his voice lower. "They were joined at their recovery point by a cruiser. When they made the jump, there was a change in course. If they remain on the current heading, they'll be here in thirty hours."

Sam nodded. This was a whole new wrinkle they didn't need. "John, did you hear that?"

"Yeah."

"We have less than an hour before we're scheduled to stop. Are you…"

"I'm good."

An hour later, they were sitting in the conference room again. Ellis tapped a key on a laptop and pointed to the large monitor at the end of the table.

"They dropped out of hyperspace right where we thought they would. Not long after, another cruiser joined them. When they jumped back into hyperspace, they had changed course."

"Are you sure?" McKay asked.

"Yes, I am. We're still tracking them. The whole fleet is on course for Atlantis."

"The Wraith can't possibly know we're here. How could they?"

"Todd didn't know our location. He never saw the coordinates and never got a look at any computers outside Rodney's lab." Sheppard said with certainty.

McKay snapped his fingers. "Yes, and both Hives destroyed each other."

"They may have picked up our distress beacon during the lockdown." Sam suggested.

"That was two weeks ago. Why didn't they check it out then?" McKay fidgeted with the coffee mug in front of him.

Ellis tapped a couple of keys on the laptop. The screen zoomed out to show the courses taken by the Hives and the cruiser. The dotted line for the cruiser indicated it traveled a long way in the general direction of Atlantis. It appeared that the rendezvous might have been planned as the quickest jumping off point to the possible source of the beacon.

"They're coming now, that's what important." John observed. He looked at Sam and Rodney. "Can you get everything done by then? Without the cloak or shield, we're sitting ducks."

"Thank you for stating the obvious." McKay snapped. "I doubt I can even get the main operating system back online by then, much less the cloak or shield. We have at least thirty hours of non-stop work. No breaks, no powering down the system. And, that doesn't even include testing to make sure we haven't screwed it all up."

"What about using the drones?" Ellis suggested.

"It's possible, but I don't know if they'll work." John shook his head. "Besides, they'd be able to broadcast our location. We'd have every Hive in Pegasus coming to the party at full speed."

"Is it possible to get just the cloak working?" Teyla asked.

"No." Rodney looked miserable. "We're screwed. We may as well evacuate and set the self-destruct."

The table fell silent for a few seconds. Finally, Atlantis' commander spoke. "It's too soon to talk about destroying the city. We have thirty hours to figure out something."

John stood up. "Colonel, can your guys beam me back to the chair room?"

"Wait a minute, John." Sam stopped him. He didn't look that great when he was released from the infirmary the night before, and now appeared to be even more drained. She caught Col. Ellis then Teyla's eyes and said, "Would you mind excusing us?"

"Of course." They said almost in unison. They left, making sure everyone else followed them out.

"We need to do this." Sheppard was suspicious of what she was going to say as he sat down again.

"I know, but we aren't going to get very far if you collapse." She knew he was right, so was she.

"I won't."

"Colonel." Jennifer Keller entered. She'd heard enough to know what he intended to do. "This is not a good idea."

"We really don't have much of a choice, do we?" He blinked and shielded his eyes from the light when he looked up at her.

"See, the headache is bad again already, isn't it?" Jennifer watched him closely as she walked around the table to sit nearby.

He turned to Sam to avoid the doctor's gaze. "It doesn't change the fact that a fleet of Wraith ships is probably going to arrive on our doorstep in thirty hours. If we don't want to either give up or blow up the city, we have to try to get the programming fixed."

Sam considered both arguments. Finally, she stood up. "Okay, John, we'll try it your way for now. Give me about half an hour. I need to talk with Rodney and Radek. We have to revise our plan of attack."

John didn't move. "You should get everyone ready to evacuate, just in case."

"Evacuate?" Jennifer asked. "The Apollo can't hold everyone, can it?"

"No." Sam responded, suspecting what Sheppard was going to suggest.

"We can send everyone to Earth through Midway. If we succeed here, they can come back. The SGC will just have to deal with the quarantine." He took a deep breath. "Rodney and I can work as long as possible. The Apollo can take anything that can't be carried and beam us out if we don't get it done."

"Colonel." Jennifer shook her head slowly, incredulous that he would even think about attempting it.

"I don't see any other option." He looked straight at Sam, ignoring the doctor's objection.

"He's right." Sam looked at her then back at John. There wasn't enough time for the Apollo to ferry the city's personnel to a safe location. It was going to take a lot more time to get a couple of hundred people through the Gate than it took for one Jumper, but they'd have to get as many out as possible. "I'll have all non-essential personnel prepare to evacuate. The Apollo can get the rest of us out."

"Sounds good." He agreed, hoping that the time needed to keep the wormhole open wasn't going to be beyond him.

Sam nodded agreement. "When do you want to do this?"

He hadn't thought that far. "Uh, let's make sure the Wraith are coming here."

"Okay. How about we evacuate if they remain on course for the next twelve hours? Is that too long to wait?" Sam hoped they might catch a break in the programming and not need to evacuate.

"No. I don't think so." He stood up and started to walk out.

Jennifer stopped him. "I want to check you out before you go back."

He was too tired to care. "Okay."

As soon as he was out the door, Jennifer turned to Sam. "How long will it take for everyone to go through?"

"Hopefully not too long." They both knew that it all depended on John Sheppard. He was going to attempt to hold the connection for the Gate active for at least thirty minutes after nearly 24 straight hours in the chair. After that was at least another sixteen hours of programming to support then, then…the cloak, the shield, weapons? Without those things, they may as well destroy the place and leave. Sam got up and walked to the door, the thought that this city might be lost on her watch weighing heavily on her. "If you'll excuse me...?"

"Of course. I need to examine Col. Sheppard and then try to decide what we can take with us." Jennifer followed, her mind taking inventory of the equipment in the infirmary. Carson Beckett drew up a list of the most valuable of the Ancient medical devices for just this kind of event. He'd discussed it with her on more than one occasion. A lot would depend on the space allotted to her on the Apollo, and it made her heartsick to think of what they might lose. One thing she wanted to take but could not was the medical scanner. It was mounted in the basic structure of the infirmary and dismantling it would take too long.

xxxxxxxxxx

Sheppard spotted Teyla on the way out. He walked up to her and spoke quietly. "You need to pack a bag. We're probably going to evacuate everyone to Earth in a few hours."

Her mouth fell open in surprise. "Excuse me? What do you mean?"

"Look, this may not work. The Wraith are going to be here tomorrow and the Apollo can't hold everyone. We're going to send all non-essential personnel to Earth through the Gate bridge. You're going." Not waiting for a reaction, he walked away.

Teyla said nothing, knowing that she would not be able to argue with him. She waited for Sam. "Col. Carter? May I speak with you?"

"Good. Teyla, I'm glad you're here." Sam had a feeling she knew what happened from the Athosian's expression and Sheppard's disappearing back. "If we haven't resolved this and the Wraith stay on course, we're going to evacuate non-essential personnel to Earth."

"John told me. He said I would be going as well."

"Yes, that's right. I'm going to make an announcement as soon as we have the PA up again."

"I wish to stay. I am sure that there is something I can do here."

Sam put her hand on Teyla's arm and shook her head once. "No, I want you to go. We're going to have limited space on the Apollo, and I don't think it would be wise to have you here if we need to run."

"Definitely not." Jennifer added them. "You're evacuating with the rest. No arguments. We have to think of the baby."

Teyla knew she was defeated by the set of both women's faces. She was deeply disappointed, but inclined her head in acceptance. "Very well."

xxxxxxxxxx

The colonel made the announcement as soon as Sheppard activated the systems again. "This is Col. Carter. We have just learned that two Wraith Hives and several support ships are on course to Atlantis. If they maintain present course and speed, they will arrive here tomorrow. If we are unable to restore the city's systems and defenses within the next twelve hours, all civilian personnel not otherwise notified will need to evacuate to Midway and then on to Earth. I'm sorry, but there won't be enough time to allow you to take personal belongings. The Apollo will be taking as much of the vital research and equipment as possible. Department heads, prepare to be beamed over to the Apollo immediately to make the necessary arrangements."

Within the hour, the Apollo settled on the east pier. She needed to be hidden there if the cloak was activated, but could easily be back in the air and make the jump to hyperspace at the last minute if the efforts to bring the city back to life failed. The provisions brought from Earth for the city were had already been offloaded. Her crew started beaming in all equipment considered the most valuable. Even though every spare inch of the ship would be packed to tight, they knew they could take only a fraction of what they wanted. The most difficult decisions were what should go and what would have to be left behind.

xxxxxxxxxx

In Gate operations, time seemed to accelerate with each passing minute. Almost nothing was said, and the dozen or so people frantically working on code barely looked up. They didn't even seem to notice the activity going on around them. Sam narrowed the focus on the main operating system, cloak, shield and weapons. Everything else could wait.

"Col. Carter. This is Ronon." He was speaking very quietly.

Four hours had passed since the last break, and it was twelve since the Wraith's change in course. "This is Carter. We're preparing to stop now."

"Good."

Ronon stepped back into the chair room and waited silently for his friend to deactivate the chair. John sat with his head bowed and his hands over his eyes for a long time. He seemed to be out of breath and energy. "John?"

"Gimme a second." John got out as he waved one hand. This city was one of the things the Ancients did right. He knew her, inside and out. He knew her soul. Right now, it was impossible to find her, and climbing out of the suffocating darkness was getting harder. Finally, he released a deep, shuddering breath and stood up. Pressing his transceiver, he said, "Col. Carter, this is Sheppard."

"Go ahead, John."

"Are the Wraith still on course for Atlantis?"

"Stand by." There was a brief pause. "Yes, they are. Sorry."

"Okay. When do you want to start the evacuation?"

"We're still getting ready here. We'll try in thirty minutes."

"Thirty minutes. Sheppard out." He actually needed hours, but that just wasn't possible. John had to settle for trying to clear his head before it imploded. He stood up and pressed his transceiver to turn off the voice activation function. John patted Ronon on the shoulder as he slowly walked out of the room. "Thanks."

xxxxxxxxxx

"I'm going to access only the Gate, okay?" John informed them when he returned to the chair.

Sam and Rodney frowned at each other. He asked what they were both thinking. "How? Can you do that?"

"I think so."

Sam raised her eyebrows at his statement. It made sense if he could do it. He'd been keeping a lot of balls in the air at once for days. Focusing on a single function might be easier. Well, relatively easier. None of this could be called easy in any context. "When you're ready, John."

A few minutes later, Chuck turned to look enquiringly at her and Rodney. They were waiting for Sheppard to give the go ahead to dial the Gate. She held up a hand, warning everyone to be patient. No one had any idea what he had to do. She wanted him to have all the time he needed so that the wormhole was stable enough for the majority of the city's personnel to evacuate.

"Try it." To their surprise, Ronon said this.

The instructions caused a whirlwind of activity.

"Dialing now." Sam said as she nodded at Chuck. He tried the first symbol. When it encoded, he quickly completed the sequence and the wormhole formed normally. The light from it bathed the waiting evacuees in its watery glow.

"Midway, this is Atlantis. Are you ready for the evacuees?" The colonel asked quickly, half regretting she'd agreed to this.

"Col. Carter, this is Midway. We're ready. Send them through." The Apollo sent word as soon as the plan was made. Midway, in turn kept the SGC informed. Since there were far too many people to keep on the tiny space station, most would go on to Earth. The SGC, in turn, had been given time to devise quarantine provisions that would satisfy the IOA.

As soon as Sam signaled to the Marine captain on the floor below, he turned to the people surrounding the Gate's raised platform. He didn't shout, but his voice was heard quite a way down each corridor. "Alright, everyone, let's go. Quickly, please."

Teyla stood up. "I hope your work is successful and we will all return soon."

"Thank you, Teyla." Sam gave her a reassuring smile. "I do, too."

"Uh, see you later." Rodney said, unable to think of anything more appropriate.

"We'll see you soon." Beth Reynolds said as she took a small Athosian made bag from Teyla. They walked down the stairs and to the Gate. With barely a glance back, they stepped through together.

"Well, at least she's safe." Rodney said glumly. After watching Teyla disappear through the puddle, he started to pace.

The formation was a little ragged, but the forward movement was orderly and quiet. Any drill sergeant would have been satisfied with discipline shown by the mass of civilians.

Progress, even though as fast as possible, was a painfully slow shuffle. All civilian personnel not necessary to the repair efforts were leaving. The teams searching for the virus laden computer were dismantled, leaving only the military to continue. Funneling them from various corridors into the relatively narrow Gate took time, a lot of time.

The military was staying. If it came to the unthinkable, the Apollo would beam them all out and take them to the Alpha site. From there, they could to Gate to Earth. It was a risk, but one Col. Carter felt warranted. She was not willing to leave Atlantis deserted while waiting for the Wraith. It was a relief when the SGC sent word the IOA concurred with the plan. They certainly didn't need a fight on that quarter.

McKay continued to pace in a tight pattern between the consoles, tablet in hand. He occasionally paused at the railing to watch the procession inch through the puddle. Each time he stopped, he became a little more agitated.

"Rodney." Sam said when he huffed past her for the third time in about three minutes.

Radek turned from where he stood at the rail. He spoke quietly. "They have only just started and are going as fast as they can."

"I think they could go a little faster if they tried. We have less than eighteen hours to go through, oh, I don't know, half a billion lines of code." He glared at the Czech then flopped into a chair. He stared at his laptop, "I just don't understand why we can't work on it at the same time."

Both Sam and Radek decided it was a rhetorical statement and said nothing.

"Col. Carter?" Everyone looked up to see Maj. Lorne approaching with a Marine sergeant close behind. A grim, but satisfied, expression told them he had news.

"Major?" She prompted.

"We think we found the computer." He slowed very briefly to allow the sergeant to pass him, and take in the evacuation below. He nodded in her direction. "Simmons found it."

McKay snapped his fingers then held out his hands and she hurried to give him a laptop. He sat down and began to search its contents, everything and everyone else forgotten. Zelenka hovered over one shoulder, trying to see the screen.

Simmons spoke to the colonel. "It was in an unused room near one of the engineering labs, Ma'am."

"Thank you, Sergeant. Well done." Sam offered her an encouraging smile. She then spoke to Lorne. "I think we need to continue the search in case there're are any others out there."

"Will do, Colonel." Lorne agreed then turned and left with Simmons.

"Rodney?" Sam turned to the chief scientist.

"It isn't one of our computers," he replied without looking up. "They probably brought it here specifically to sabotage us. Give me a minute."

Reluctantly, she turned her attention to the exodus. More than ten minutes had passed and there wasn't even a dent in the number of people she could see on the floor below and up the corridors visible from this angle. Her eyes flicked from the Gate to the Gate controls, looking for any sign of change in the stability of the wormhole. This was going to take far too long.

"Get a move on, people!" The captain's voice boomed throughout the huge space. The movement of the evacuees sped up only a fraction. They were actually moving as fast as possible. Just as the Gate was wide enough to accommodate only a handful of bodies, there wasn't a lot of room in Midway for arrivals to quickly spread out or move through the Milky Way Gate. He felt, however, the encouragement to keeping moving couldn't hurt. "We don't have all day."

Sam looked over through the railing again. Time was dragging now. Too slowly.


	9. Chapter 9

**Chapter 9**

"I think so," Sheppard said then turned off the vox on his transceiver. He hoped he could activate only the Gate this time. Not having to connect so many systems would give him a better chance at keeping it running for however long they needed to move out the now sizeable population in Atlantis. He looked at Ronon and pointed to one of the monitors. "When that lights up, tell them to try it."

Now he had to find his way to just those connections. There was no metaphorical light in there, no sound or sense of feeling, nothing to show him the way. The primary reason he'd been activating so many functions was that it was close to impossible to isolate any one or more of them. Only using the Gate to send the away team to the Alpha site gave him any sense of what to do. This was going to be hellish.

With a deep breath, he sat down and placed his hands on the pads. The chair lit up and reclined immediately.

After several seconds, Ronon realized nothing was happening. There was no sound from the Gate room and the monitors in the room around him were still inactive. He peered at Sheppard, who was absolutely motionless except for deep, rhythmical rise and fall of his chest as he breathed. He pushed away from the wall just as Sheppard took a deeper breath and the monitor came to life.

"Try it."

The distinct sound of the Gate dialing and the wormhole forming could be heard over their transceivers. Ronon had trouble making out the muffled voice in the background, but he knew it was Capt. Travis starting the evacuees moving. Now, he could only wait until the all clear was given and Sheppard could shut it down.

Time slowed again. It moved at a snail's pace every time John sat in the chair. Ronon knew McKay probably had some incomprehensible explanation for it. He disliked wearing a watch. His internal sense of time was normally quite accurate, but being in this dark, windowless room and waiting hour after hour was messing that up. He rolled his shoulders in an effort to loosen muscles tight from inactivity and tension then settled down to wait some more. After what he figured to be a little more than half an hour, he heard the Gate shut down.

"John, this is Carter." There was a long pause. "Col. Sheppard, this is Carter."

Ronon realized Sheppard wasn't going to respond. He didn't even seem to be aware Sam was speaking. He touched his radio and spoke quietly. "This is Ronon. Sheppard has his radio off."

"Tell him everyone has been evacuated. We've shut down the Gate."

"Okay." He turned off the vox as he walked over to the chair. There was still no sign Sheppard heard the exchange. He put his hand on his friend's shoulder. "John?"

The hazel eyes opened slowly, but were unfocused. He blinked, trying to clear his vision. "Hmm?"

"They're all at Midway. Carter said you can shut it down."

John lifted his hands and the chair immediately deactivated. He slowly stood up, but staying upright was not easy.

"Sheppard?" Ronon bowed down slightly, trying to get a better look at him.

"I'm good. That was easier than I thought." He nodded and flashed a weak grin at the Satedan then tapped his radio. "Col. Carter, this is Sheppard."

"Good work, John. How are you doing?"

"Not bad. You?" His flippant response didn't come off quite right.

It was a moment before she answered. "Fine, thank you.

"When do you want to start again?"

"Give us few minutes. We found a laptop that may have been used to introduce the viruses to the system. Rodney thinks he may have something."

"Sure." John's voice was a whisper. He sagged against the wall, sliding down until he was sitting on the floor. Blowing out a ragged breath, John wearily rubbed the back of his neck.

"I thought you said it was easy." Ronon stated as he joined his friend, handing him a bottle of water.

"Easier than I thought it would be." John's voice was raspy. He took the water, swallowed several mouthfuls then cleared his throat. Closing his eyes, he leaned his head back.

"How's the head?" Ronon asked.

"Still there." Sheppard pressed fingertips into his eyebrows. "It's not too bad."

"Right." Ronon said without believing him. He wanted to say more, but knew it wouldn't help.

After a couple of minutes, John pushed himself up, using the wall as support. Ronon jumped up, ready to help but was waved off. Walking stiffly to the door, John knew he got a severe frown even though it was too dark to see it. "I need to stretch my legs before we get going again."

xxxxxxxxxx

"Rodney?" Sam prompted about fifteen minutes later. He'd been hunched over the laptop since it arrived, waving Radek away more than once.

"Yes?" was the only reply.

"Rodney." She said a little more firmly.

This time he glanced up, a glimmer of hope was visible in his bloodshot eyes. "We may be in luck. I think I can use this copy of the virus to finish the worm and restore the main operating system."

"Really? How long do you think it will take?" Sam's mind was sent racing. If he could pull this off, how much longer would it take to get the shield and cloak?

"A few hours. Maybe eight." McKay said absently then looked up at her again. "Be happy I can do it that fast. This is huge."

"Should we keep working on the shield and cloak?" Zelenka asked.

McKay frowned at the Czech, the long frantic days showing on his face. They were all like that, tired in body and mind. "Yes. No. I think I can adapt some of this. It'll be faster. Just let me work on it."

"Okay." Sam agreed as she grabbed an idle laptop left by one of the evacuated technicians. She could keep it isolated from the system while working through the offending programming. "I'll help. Copy it over for me."

"And, me." Zelenka picked up another laptop.

He sighed and muttered, "Waste of time."

Sam tapped her transceiver and said, "John, we're working on the worm. It's going to be a few hours before we need you again. Get some rest."

xxxxxxxxxx

Dr. Keller watched her patient as he slept. She wanted to call a halt to it and said as much when Sheppard was beamed into the infirmary earlier. Even in such a debilitated state, the colonel was stubborn and persuasive, and intimidating. The conversation was short and ended with her relenting. She wasn't happy.

"Col. Sheppard?"

John turned his face into the pillow, trying to shake off the dream that kept intruding on his sleep. He felt he knew the disembodied voice that chased him, but couldn't quite place it. The pounding in his head was incessant and threatened to drown out everything going on around him. Even sleep was not helping now.

"Col. Sheppard." This time the voice was accompanied by something on his shoulder.

"Wha'?" He grunted then opened his eyes.

John had been spirited to the infirmary immediately Sam told him to rest. Once there, Jennifer insisted on another scan and checked his heart, lungs and eyes. When she wouldn't let him go to his quarters to sleep, he pulled off his boots and transceiver and lay on the bed he'd recently occupied. The holster and shirt were discarded when they started the examination. She shook her head in quiet exasperation and gently drew a blanket over him.

Jennifer smiled hesitantly at him. "I'm sorry to have to wake you, but Col. Carter says they're going to need you in a little while."

"Course they will." John muttered under his breath as he rolled to a sitting position on the edge of the bed. The movement was too fast, sending his head and stomach spinning. He clutched the edge of the bed just as she grabbed his arm. It was a full two minutes before the room began to slow and right itself.

John reached up to turn on his transceiver only to discover it was gone. He rubbed his eyes and blinked at the bedside cabinet. The room was thankfully dim, but it made it difficult to see anything. Keller realized what he was looking for and handed it to him. He looped it over his ear. "Thanks."

"Sorry, I need to…" She pulled a wheeled table over. A blood draw kit was on it.

He peered at her for a moment, taking some time to understand what she meant. His eyes followed her hand to the table. He winced then nodded and offered his arms. She hesitated before choosing the left. Both arms looked like pin cushions already, but the left a little less so. A couple of minutes later, two vials of blood lay on the tray and the used kit was in the hazardous waste container.

Jennifer then put on her stethoscope and placed the diaphragm over his heart. The quiet in the nearly deserted infirmary and thin t-shirt made listening easy. She heard the strong, if slow, beat. Jennifer quickly followed that by taking his blood pressure and temperature. Both of those were on the low side for him. She wasn't happy, but was also not surprised.

"All finished." She said with an encouraging smile. "Do you want something for your headache?"

He didn't trust his head to stay on if he shook it, so he just said, "No."

She stepped to one side, but stayed close. "Col. Carter asked if you could go to the control room first."

John carefully slipped off the bed. When he started to bend down to pick up his boots, the doctor beat him to it. She handed them over and directed him to a nearby chair.

"Thanks."

xxxxxxxxxx

McKay was shocked at his friend's appearance. He hadn't seen Sheppard in more than 24 hours and was appalled at his appearance. He blurted, "You look terrible."

"Thanks, Rodney. You don't look too good yourself." Sheppard gave him a sidelong glance through barely open eyes. The light was murderous and tunnel vision brought on by the migraine threatened to block his vision entirely. He needed to get out of there quickly.

"I was just saying…You've gotten a lot more sleep. You should be…" The astrophysicist stopped when Sam nudged him. He frowned at her. "What?"

She ignored him and spoke directly to John. "I'm sorry to bring you up here. I want you to know where we stand."

He blinked at her, trying to clear his vision. "Sure. What's the plan?"

"We think we've modified the virus on the laptop found earlier so that it will, well, undo the damage caused." Sam wanted to keep the explanation as simple as possible. She knew John was having difficulty standing, much less thinking right now.

"That's a little simplistic for the complex…" Rodney started.

"Yes, Rodney, but we really don't have time to go into the details right now. Do we?" She cut him off and looked back at John. "It's going to take a while to load and run it."

"How long?" John asked.

"Two hours tops." Rodney squirmed a little at the disappointment in Sheppard's eyes. "Well, like I started to say, it's incredibly complex. And, it's huge. I have to be certain it loads all in one hit or we'll have to start over again." He shrugged apologetically. "We can't rush it. I'm sorry."

"Can you do this?" Sam spoke to him quietly. The chances that it was going to work at all were slim, and it rested completely on this man's ability to hold his concentration for the time needed. Right now, she wouldn't have bet money on it. She was surprised Jennifer hadn't stopped the whole thing days ago.

John thought for a moment then nodded. "Is that it?"

Sam and Rodney glanced at each other. She spoke first. "No. We'll need to test it, and this is just the main operating system. We still need to work on the cloak and shield."

"And, the drones." Zelenka reminded them.

"Yes. Thank you for that." McKay snapped. He checked his watch. "The point is, we still have a lot of work to do, and we have only seven hours and ten minutes to do it in."

Sighing, John blinked slowly. "Anything else I need to know?"

"The Apollo has started beaming over the equipment we're taking. All personnel except the five of us will follow thirty minutes before the Wraith get here. We'll keep working as long as we can." Sam paused. "But, if this doesn't work, Radek will pull the ZPM then Col. Ellis will beam us out and nuke the city as the Wraith come out of hyperspace. At that point, there will be no discussion."

"Uh, we'll let you know when it's back online." McKay offered lamely.

"I'll know." John touched his transceiver. "Apollo, this is Sheppard. Can I get a lift to the chair room?"

xxxxxxxxxx

John was getting used to the suffocating feeling but dreaded entering the darkness. He just had to remember it was in his head and to keep his lungs moving, drawing air in and pushing it out. That was one of the difficult parts. It would be too easy to get lost in it. A fear niggling at the back of his mind whispered he soon might not be able to find his way back.

It was almost fours before Sam radioed he could power down.

"Sheppard." Ronon said firmly, but quietly. There was no acknowledgement. He'd worried this was going to happen again. Quietly approaching the chair, he laid his hand on John's arm. When there was still no reaction, he gently squeezed. "Stop. Carter said so."

John suddenly opened his eyes, staring straight ahead and gulping in air like a drowning man breaking through the surface of a vast ocean. He deactivated the chair and looked around before realizing the Satedan squatted next to him. Breathless and disoriented, he asked, "What happened?"

"Nothing. Carter just said you could power down, that's all. Are you okay?"

"Yeah." John scrubbed his face with shaky hands. He blew out a long steadying breath before speaking again. "I'm okay."

"No you're not." Ronon said with some bitterness. It felt like he was sitting by and watching his friend slowly kill himself and it was intolerable. He just didn't know how to help. "Sheppard…"

"We're almost done." He said hoarsely. They were too close to either saving the city or destroying her. John was determined it would be the former. He tried to clear his throat then activated the transceiver. "Col. Carter, this is Sheppard."

"Go ahead, John."

"Did it load?" John leaned heavily on one arm of the chair.

"Yes, it did. We have some problems, though. We need a little time to figure out what went wrong."

"Do you want me to start her up again?"

"Not yet. Give us a few minutes."

"Take your time." John said with relief then turned the vox off. He tried to stand, but his legs didn't seem to know what to do. Ronon grabbed his arm and helped him up. He silently nodded his thanks.

The sound of his own voice in his head felt like someone was screaming in his ears. He unhooked the transceiver and stuffed it a pocket. Ronon would let him know when Sam radioed again. He was glad it was Ronon, the man of very few words, with him.

His stomach was beyond redemption and his entire body ached, but movement seemed the only way to stay alive. As shaky as he felt, and since there was no time to find relief in sleep, John figured the only thing he could do now was to move, get his blood flowing again. Progress was slow. He stayed close to the wall and frequently reached out to touch it. Ronon knew the headache was affecting his vision and suspected it was worsening.

"You should rest." Ronon said when he stopped and leaned against the wall for support.

"No." Sheppard grunted as he straightened and began walking again.

Half an hour had passed before Sam called them.

"Stand by." Ronon wiggled a finger at his own ear to let him know.

John blinked in confusion before realizing what he meant. He reached up to activate his transceiver to find it wasn't there. Disobedient fingers fumbled when he pulled it out of his pocket and tried to put it on.

"Ronon, please let John know we need to tweak the programming a little. Can he bring the system up again?"

"Sure. We're on our way back now." He saw that John had given up trying to hook the radio over his ear and just held it against his ear.

"Where the hell are you?" McKay demanded loudly. "We're on a clock here."

"God." John groaned as he staggered, dropping the transceiver while blindly reaching for the wall. Ronon barely caught him as he fell. He felt a cold sweat on Sheppard's skin as he lowered him to the floor, his back to the wall for support.

Sheppard tried to ease the pain by pressing trembling fingers against his forehead. He didn't hear the muffled admonishment from Sam or the whispered apology. It was several minutes before he could speak or move. Finally, he nodded and tried to stand. Ronon helped him to his feet, snatching up the transceiver as he did so.

He carefully looked around. "You have to get me back to the chair. I can't see anything."

"You have to stop." Ronon kept hold of his arm but didn't move.

John tried to look at him. His was voice low and hoarse. "No. We're too close. Get me back."

"It's not worth killing you."

"It won't. Take me back. Please."

"Okay."

xxxxxxxxxx

Sam tapped her radio and glared at her chief scientist. "Rodney!"

He already knew what he'd done. The strangled exclamation from Sheppard caused him to blanch with horror.

"What is wrong with you?" She was livid. Exhaustion and stress were not an excuse, even for the highly strung genius. Apart from the fact they needed the colonel to have any hope of saving the city, the pain inflicted was unforgivable.

He whispered miserably. "I'm sorry. I didn't know he…"

"You'll have to apologize to John." She exhaled heavily and turned to her laptop. "Now, just…be quiet."

He started to say something, but the set of her jaw made him stop and turn to his own computer. They waited in silence, knowing Sheppard would either activate the systems or Ronon would let them know he couldn't.

After several worry-filled minutes, the city came to life again.

The little remaining time flew by. Even though very few words were spoken, the tension in control room grew oppressive.

"Col. Carter, this is Ellis." They jumped at the unexpected sound.

Sam checked the time. They were down to an hour and nowhere near finishing. "This is Carter."

"The Wraith are still on course. We've finished loading the equipment. Should we start beaming out personnel as planned?"

"Damn it." She muttered under her breath. "Yes, I think we have to. Stand by, please."

"Standing by."

She turned to the technician at the communications console. He depressed a key and nodded. "This is Col. Carter. The Apollo is going to start beaming out all remaining personnel immediately. Be prepared to leave according to plan. Thank you."

Civilian personnel would go first. The military would start beaming out thirty minutes before the deadline. Squads guarding the Gate room, the ZPM and the chair room were scheduled last. They would wait until the last minute for Col. Carter, Sheppard, McKay, Ronon and Zelenka. There was going to be little room for error.

Sam nodded to the technician who turned off the PA system again. She looked around at the various staff still working around her. "Thank you, everyone. You'd better grab your gear."

"Thank you. Good luck." The young woman next to her said as she got up and headed for the stairs, picking up a small bag from a nearby chair. She was followed by the others.

Sam took a deep breath. "Col. Ellis, whenever you're ready."

"Commencing beam out, Colonel." The Apollo's commander responded. "We'll keep you apprised of our progress."

Fervent prayers to every deity known to the relatively few remaining inhabitants of the city were offered up as the Apollo's beam began transporting people to the ship.

"Thank you, Colonel." Sam exhaled heavily and focused on her computer again. "John, come in."

"This is Ronon." His deep voice was almost too quiet to hear. "Sheppard doesn't have his radio on."

She wasn't surprised after McKay's outburst. "How is he doing?"

"Hard to say."

She winced, but understood what he meant. "The Wraith will be here in an hour. We may have to pull out, but I'll let you know."

"Okay."

Sam mentally shook her head. Conversations with Ronon were even more frugal than those with Teal'c. She rubbed tired eyes and squinted at the computer screen

Rodney finally straightened and lifted his hands from the keyboard. "I think we can try it again."

Zelenka looked up. "Really? Are you sure?"

"Yes, I'm sure." He replied in an exaggerated and exasperated whisper. He turned to Sam and whispered more softly. "You want to tell Sheppard?"

"Ronon?" Sam also spoke quietly.

"Yeah?"

"Tell John he can shut it down. We're going to try this again."

"Okay."

It was a full minute before the systems went down.

McKay wiped a sweaty hand on his shirt then reached across to ATA pad. He released a deep breath and lowered his hand onto the pad. Nothing happened. He swallowed hard and wiped his hand on his shirt again then he put it back on the pad. Nothing.

"Oh, come on! It has to work." He stood up and used his other hand with the same result. Glancing at his watch, he moaned, "We have 28 minutes."

"That gives us 28 minutes to keep working, Rodney." Sam frowned at him then back at her computer. "We need to keep trying."

"Yes, of course we do." He dropped back into his chair, hunching over the keyboard.

"Radek, you'd better get down to the ZPM room."

"Yes, Colonel." The Czech was to retrieve the power source at the last minute. He touched his transceiver. "Col. Ellis, this is Zelenka. I am ready to beam."

"Beaming now, Doctor." A moment later, he was gone.

All too quickly, Ellis radioed, "Col. Carter, this is Ellis."

"Go ahead Colonel." She exchanged harried glances with Rodney.

"We have everyone on the Apollo except the Marines guarding the Gate room, the ZPM and the chair room. We're powered up and ready to leave."

"Thank you." She nodded her thanks. "We'll know in a few minutes."

"Standing by."

"Maj. Lorne, this is Carter."

"This is Lorne, Colonel." The major responded immediately.

"Take the Jumpers out of blast range, Evan."

"Yes, Ma'am. We'll be cloaked before the Wraith drop out of hyperspace. Good luck." Lorne was to lead all Jumpers away from the city. They would move well out of range of the shockwave and radiation created by the bomb. If the city was destroyed, the ships would be left cloaked on the mainland for the Apollo and Daedalus to collect later.

"Good luck."

"Are you ready to pull the ZPM, Radek?" Sam said.

"Yes, Colonel." He replied. This was to be his, and Sheppard's, last task in Atlantis.

"And, you have the crystal from the DHD?" She asked Rodney. The crystal for dialing Earth was useful elsewhere. He nodded desolately.

That was the last of the housekeeping. There was only the miracle left to perform.


	10. Chapter 10

**Chapter 10**

"Ronon, please ask John to power up again. This will take only a few minutes."

"Stand by." The Satedan turned off the vox and walked to the chair.

Sheppard was sitting forward, resting forearms on his knees and head bowed low. He'd decided it wasn't worth the effort to move, and realized he probably couldn't walk more than a few steps anyway. With so little time left, they would need to try again soon or not at all. Ronon touched his shoulder and dulled eyes looked up.

"Now?"

"Yeah. Carter said it won't take long. The Wraith'll be here soon."

John released a deep, shuddering breath as he sat back. He let go of the light and sound and descended into the darkness. She was still so quiet, not even breathing. What he was doing was only life support. He was only keeping her heart beating, and he couldn't do it much longer.

Ronon stood close by and watched his friend. He could hear Sam and Rodney talking quietly, but their conversation was in fast gobbledygook. None of it made any sense to him, but he did understand the growing desperation and resignation. The conversation slowed to a stop, ending with a groan from McKay.

"We have eight minutes, Rodney." Sam's voice came over the radio.

"We have to try."

"It's going to cut it very close."

"I know. We can do this." He pleaded.

Sam raised her voice a hair. "Ronon, tell John we want to try again. He can power down."

"Okay." He squatted down next to the chair. "Sheppard. Carter said to power down."

There was no response again so he firmly squeezed John's arm. The skin under his hand was cold and clammy. "John, let it go."

Sheppard took a deep breath and nodded. A moment later, his hands moved just far enough to go off the pads. The chair returned to the upright position and the power went off. He looked at Ronon, but could only make out a vague shape. "What's going on?"

"Carter and McKay are trying it again. If it doesn't work, the Apollo's going to beam us out in a couple of minutes. We're out of time." His voice was rough with anger and disappointment. All of this for nothing.

"How much time?" John searched his pockets for the transceiver.

"Did you hear that?" Ronon spoke into his mic. He handed the radio to his friend.

"Yes. Six minutes. We'll be ready in two." Sam answered grimly. "The Apollo will beam us out at the two minute mark."

"Wraith'll be here in six minutes but the Apollo's going to beam us out in four." He watched as John slowly worked the transceiver over his ear.

"Okay."

xxxxxxxxxx

"Damn it. There's the problem." Rodney hissed between clenched teeth and began to type furiously. "I found the problem. I can fix it."

"Rodney, it's too late. We have to go." Sam said urgently. "Col. Ellis, I…"

"I can do this! I just need a few minutes."

She peered over his shoulder to see what he was doing. "We don't have enough time. We have…"

"Wait. Wait." Sheppard interrupted her with as much force as he could muster. He fought to think straight. "How much time do you need, Rodney?"

"Just a few minutes. Five, six, no more. I'm certain."

"Are you sure?"

"Yes!" he replied in a frantic whisper. "Yes, I'm positive."

"Then do it."

"John." Ronon began.

Eyes tightly closed, he shook his head once and took several deep breaths.

"What are you doing, John?" Sam asked, already knowing the answer. She added, "We have less than three minutes. We have to go."

He'd already reactivated the chair and all of the systems. "Rodney, the cloak."

xxxxxxxxxx

McKay instantly reached across and hit the control.

"Now fix it." Sheppard's voice was a strained whisper.

"What is going on?" Ellis and Zelenka asked simultaneously.

"Col. Carter, this is Lorne. The city just cloaked." Station keeping out of blast range, he had a perfect view of the city just before it vanished. "Nothing showing up on the HUD, either."

Ellis confirmed the report. "He's right. The cloak is working and…stable. Your call, Colonel."

She glanced at her watch, calculating the time left to them and how long it would take to beam everyone out, get the Apollo in the air and bring up her shield. Not enough.

"A hyperspace window is opening." Lorne announced. The Apollo was now effectively trapped. Even though the massive ships and their escorts emerging from the wormhole were some distance away, the combined fire power would be able to destroy the Earth ship if they detected her. They were here because they suspected something and probably had weapons online, a fact soon verified.

"Col. Ellis, it looks like we stay put." Sam made it official. "If anything happens, get out of here."

"If anything happens, we'll all get out of here." His tone made it clear there would be no arguments.

"Thank you, Colonel."

"It looks like they're all here. We have two hives, fivers cruisers and four support vessels." Lorne counted off the fleet.

A few seconds later, Ellis added, "The Hives and cruisers have weapons powered up."

Sam rubbed the back of her neck. "Let's hope they leave quickly."

And, they all thought, that Sheppard could keep it together for as long as it took. It all depended on a single, exhausted man.

They waited. It was an agonizing period of time, interspersed with commentary from Ellis and Lorne on what the all too numerous Wraith ships were doing. The grounded Apollo used the eyes given her by Asgard technology. The Jumpers, all piloted by experienced military personnel, tracked ships sent to the mainland.

The suspicion that they were investigating the possible source of the signal detected by the cruiser tens of thousands of light years away grew as the search progressed. The humans hoped the Wraith would quickly decide the point of origin was not this planet after all.

xxxxxxxxxx

Ronon took up his vigil again, standing motionless next to his friend. He knew John was at the end of his endurance. His breathing was fast and shallow, and even in the dim light, it was easy to see there was no color left in his face. The minutes ticked by slowly for everyone. Apart from the occasional report on the movements of the enemy ships, the only sound was the ocean in its perpetual motion.

To the humans on Atlantis, the Wraith seemed to dawdle in their search. It was, however, actually brief. The Hives and two of the cruisers ran a quick pattern over the vast ocean while the remaining cruisers and support ships raced to the mainland.

The Puddle Jumpers flew to high orbits so that they could track the various Wraith vessels without trying to keep up or travel too far from the city. Updates of their positions were cursory and mostly sent in data bursts directly to the Apollo. None were transmitted to Atlantis' computers for fear of overloading an already tenuous connection.

Ronon knew a lot of time was passing. John's breathing was becoming erratic. He was trying to trying to slow it down and keep it steady but it was a struggle.

"I'm finished." Rodney whispered.

Sam asked in an equally low tone, "Are you sure?"

"Yes."

A moment later, minor functions began to go offline.

"Oh, God." Rodney choked out in terror.

"Col. Carter, this is Ellis. We're reading changes in the city."

"Stand by."

"What's going on?" Ronon whispered into his mic as he watched Sheppard.

"Is John okay?" Sam asked immediately.

"No. What's going on?"

"He brought most of the city's functions online earlier. They've started shutting down."

"Sensors show the cloak is holding steady." Ellis reported. "What do you think, Colonel?"

Ronon could hear McKay snap his fingers. "Sheppard may have shut down those functions on purpose. Less to do."

"True." Sam agreed. "Ronon, how is he?"

The Satedan backed up a couple of steps before answering. "Not good, but he's doing what he needs to."

"Okay. First sign…"

"Yeah." He understood.

"What do you mean, first sign?" McKay asked.

"Later, Rodney." She hissed.

"What?" He connected. "Oh."

Col. Ellis, did you follow that?"

"Yes."

"We'll wait it out."

"Acknowledged."

Almost an hour went by before the Ellis reported. "The Hives are leaving orbit."

Lorne followed immediately with, "Col. Carter, the cruisers are heading out. It looks like they're on course to rendezvous with the Hives."

"A hyperspace window is opening." There was a long pause before the Apollo's skipper continued. "They're gone."

Sam breathed a sigh of relief, but needed to confirm they were safe. "Are all ships accounted for?"

"Yes, Colonel. All of them. No darts were launched and none of the ships landed." Ellis responded. Telemetry from the Jumpers confirmed the last statement. Once the planet was determined to have no Gate or any obvious signs of life that might be human, the Wraith moved on.

"Thank God." Rodney breathed, slumping in his chair.

"John, I think we're in the clear. You can power down." Sam said quietly, hoping she was right.

Ronon squatted down next to his friend. He believed Sheppard could hear them, but it was another matter if he was really aware of what she said. John's breathing had steadied somewhat since he turned off several functions, but it was still labored.

"John, the Wraith are gone. You can stop now." Ronon waited, hoping the message was getting through. It had been more difficult each time to get him back from wherever he was. He raised his voice. "John, let it go."

"Ronon, what's happening?" Sam asked.

"I don't know. Can I just pull him off the chair?"

"No. We don't know what that would do to him or the city." McKay replied quickly.

"John, snap out of it!" He grabbed his friend's shoulder and squeezed it. When there was no reaction, he increased the pressure. Sheppard drew in a sharp breath and opened his eyes. He gasped for breath and looked around but didn't seem to be able to see anything.

Ronon frowned at him. The chair was still active and Sheppard didn't appear to know he was there. After several seconds, his eyes closed and he lay back again. Without any warning, the chair started to turn, causing Ronon to scramble backwards.

xxxxxxxxxx

"What the hell?" McKay said as he looked at the consoles around him. Sam mirrored his confusion and movements. One by one, the controls were initializing, even those for minor functions that hadn't been used since the invasion by the viruses. After watching with mouths open in surprise, they turned to their computers, trying to determine what was happening.

"Col. Carter, this is Lorne. The cloak has dropped."

The pair was startled when one of the Ancient monitors behind them came to life. The image showed the Wraith armada moving along the course set on its jump into hyperspace.

"Apollo, are you tracking the Wraith?" Sam asked.

"This is Ellis, they're still in hyperspace and maintaining course."

"Thank you, Colonel. Our sensors seem to be working." Sam wondered if this sudden activity was a good or bad thing. Was Sheppard finally losing control? "Maj. Lorne, I want you to keep the Jumpers at a safe distance for now."

"Yes, Ma'am." He said hesitantly.

"Ronon, do you know if John is doing this?"

"Did you activate the shield?" Ellis asked with surprise and suspicion.

"No." Rodney answered with growing alarm. "What the hell is he doing?"

He and Sam stood up to peer through the door to the balcony and saw the shield's glow discolor the early morning sky. They quickly turned back to the computers, trying to figure out why the shield was up. The monitors registered normal power levels throughout the city. Lights, transporters, and all other functions were coming online.

"Drones! Two drones have launched." Lorne reported, his own voice now registering alarm.

"What are they doing?" Sam stared at Rodney. This was unexpected.

"They're flying out over the water, away from the city. Wait. They've collided. Both have been destroyed." Relief and confusion registered in the major's voice.

McKay shook his head in disbelief. "What the hell is going on?"

Sam suddenly realized what Sheppard was doing. "He's running a systems check."

"He can't be. Can he?"

"The shield is coming down." Sam said as she studied the monitor. "It has to be."

Suddenly, everything went offline again. Lights, computers, everything went dead. Sam and Rodney looked at each other in horror, holding their breath. After sitting in the quiet for several seconds, they turned to their computers, but there was nothing they could do.

"Oh, God." Rodney said in a whisper.

They both jumped when all systems initialized, starting with the main operating system then all other functions in quick succession. It was like some giant switch was magically flipped and the city was alive again.

"What's happening?" Radek's question sent their fingers flying on keyboards.

"Stand by." Sam replied as she and Rodney worked. They quickly ran through a checklist of the major systems. One by one, it appeared that all were working normally. Sam shook her head incredulously. "He did it. Radek, it looks like we're good, but would you mind staying put for the time being while we confirm?"

"Certainly. Should I run diagnostics here?"

"Give us a few minutes." She said, wanting to run diagnostics from the control room first.

"Everything appears to be stable." McKay stated after studying the readouts. "The programming seems…Wait. The chair's been deactivated."

They looked around then checked the computers again. All systems continued to work normally.

Tentative relief was replaced by deep concern. "Ronon, do you read?"

xxxxxxxxxx

Sheppard tried to get up but discovered his muscles didn't understand what he wanted to do. His head felt like it was about to break open and he vaguely thought that it might be better if it did so the little man pounding to get out actually got out. It didn't even alarm him that he couldn't see anything more than hazy shapes. A buzzing sound in his ears had grown so loud it was impossible to understand what was said. Even Ronon sounded muffled and far away.

"John!" Ronon grabbed him as his attempt to stand failed.

"Ronon, what's wrong?" Sam asked.

"He needs a doctor! Now!" He held his friend up. "Hang on, buddy."


	11. Chapter 11

**Chapter 11**

"Col. Ellis…" Sam started.

Ellis nodded towards the officer on his right. "Already on it. We'll beam him to the infirmary now."

"No! Wait! I have to get Col. Sheppard under the scanner. I need to know what's going on." Jennifer suspected John would end up causing himself serious damage and came to the bridge to monitor the conversations between the Apollo, Atlantis' control room and the chair room.

They had no idea what the near continuous interaction with the disabled city would do to him. The boost in his synaptic activity was a little too reminiscent of Rodney's experience with the ascension device. The last few scans indicated that the effects were dissipating at a much slower rate. The fact that he went back to the chair with only a short break didn't help. Her protests regarding Sheppard did not fall on deaf ears, but his argument that he could continue, had to continue, were more persuasive.

"Your staff is here on the Apollo." The colonel reminded her.

"Beam me and Col. Sheppard to the infirmary now. Only Dr. Cole and two nurses are here. Send them next." She didn't want to waste time. "Colonel, please."

"I agree, Colonel." Sam broke in.

"Okay." He said with a good measure of uncertainty, but the infirmary had power and the equipment she needed. The Wraith were gone and the city was back online. He was not going to argue. "Ronon, we're sending you to the infirmary now."

xxxxxxxxxx

The Apollo's beam deposited the doctor in the infirmary an instant after the two men. Ronon held a nearly unconscious John at his side.

"In here." Jennifer pointed him to the scanner room. "What happened?"

"He just collapsed." Ronon replied as he effortlessly picked up his friend and carried him to the bed under the scanner.

She placed her hand on John's forehead and cheek for a moment. His skin was cold, clammy and a frightening color. He groaned and tried to turn away from the light. She pulled open his shirt and, with practiced speed, cut down the length of the t-shirt underneath. Putting on her stethoscope, she listened to his heart and lungs. His breathing was fast and shallow and his heart was racing.

"Col. Sheppard? John?" There was no reaction when she firmly shook his shoulder then rubbed her knuckles on his sternum. She pulled a pen light from her pocket and flicked the light across his eyes, closely watching the reactions. At least that was normal, she thought. Jennifer glanced up at Ronon. "He's unconscious. What happened before he collapsed?"

"Nothing. He just tried to stand up. What's going on?"

"Come hold him for me." She showed him how to hold John's head straight for the scan. As Ronon took over, she hurried to the scanner controls. "What about the headache? Was it getting worse?"

"It was really bad and getting worse." He didn't hesitate to tell her what she wanted to know. "You know he started puking yesterday, don't you?"

"No, he didn't mention it." She said suspiciously. "Anything else?"

"I think he was having trouble seeing."

"Damn it. I was afraid of that." Jennifer switched on the scanner and it started the steady sweep down his body. She stopped its progress, holding it over John's head. "Oh my God."

It was a whisper, but Ronon heard it. "What? What's wrong?"

At that moment, Dr. Cole rushed in, followed by Marie and Alex. Jennifer dragged her eyes away from the monitor for a bare second. "Marie, get an IV going. Normal saline for now. Alex, get a gurney. Once we have him in bed, I want oxygen on him for now, as well."

"Yes, Doctor." Both nurses said as they disappeared through the door. They returned within seconds, but waited while the scan continued.

"Jennifer, what happened?" Dr. Cole asked as she peered at the monitor.

"I'm not sure." She compressed her lips and shook her head. "I just don't think human beings are supposed to be using the Ancient technology like that for such a long period of time."

"What do we do?"

At a loss for how to treat her patient, Jennifer threw up her hands and shrugged. "I don't know. I've been searching the Ancient database for any information about how prolonged use of the technology affects humans, but there's nothing."

"Well, the Ancients were probably the only ones using the technology so there might not be any data." Dr. Cole suggested.

"That's what I was thinking." Jennifer stopped the scan and they checked his vitals again. The results were only marginally better. "Well, at least his breathing and pulse are slowing down. His blood pressure is low, but not significantly so. I think the only thing we can do for now is keep him hydrated and comfortable."

Alex pushed the gurney to the bed. He and Ronon swiftly transferred the unconscious man to it.

Jennifer stopped Ronon as he tried to follow when Alex and Marie moved Sheppard to the next room. "Let us do what we need to do. I'll call you as soon as I know something."

He scowled at her for a second then nodded and left.

Jennifer followed her patient to the other room. Dr. Cole and the two nurses were already removing his BDUs and dressing him in scrubs. As she readied the heart monitor, she instructed them, "I want him on his side. Ronon said he's been vomiting and I don't want to risk aspiration."

xxxxxxxxxx

The Apollo began beaming personnel back into the Gate room as soon as Col. Carter gave the go ahead. First and foremost, she wanted to confirm the viruses had been eradicated and all systems were normal. Ensuring the city was safe had to be their top priority for now. Zelenka was brought back from the ZPM room and was quickly followed by those transported to the ship.

At McKay's stern orders, everyone was to do nothing but review code. At the first sign of trouble or if anything questionable was found, they were to let him know immediately. The threat of his displeasure, however, was less of an incentive to obey than the thought that Col. Sheppard was in the infirmary.

Leaving the Jumpers parked near the Apollo, Lorne and the other Jumper pilots materialized on floor in front of the Gate. He ran up the stairs, two at a time and walked to where Col. Carter was working. His smile was tentative. "Good to see we're still here, Colonel."

"It is good that we're still here." She said tiredly. "Evan, we still need to confirm that all traces of the viruses have been removed and systems are functioning normally. Let's leave the Jumpers where they are for now."

"Yes, Ma'am. I take it you're not recalling anyone from Midway just yet." He said.

"No, not yet."

"What are your orders, Colonel?"

"Security in sensitive areas has to be reestablished." She paused. "We still need to sweep for computers, too. All our computers are accounted for and will be scanned, but there may be another unauthorized one out there."

"That's a scary thought. I'll start assignments as our people are beamed back."

"Thank you." She nodded. They both noticed Ronon approaching. "How is John?"

"Don't know. Keller has him in the infirmary."

"Well, is he talking? Is he up and around?" McKay asked anxiously.

Ronon leaned against the back side of the console where they were working. "No, he's unconscious."

"What did she say?" the scientist pressed him.

"Um, she said his vital signs aren't good but getting better. There was something about the scan, but I don't know what it meant." He scowled at the lack of real information. "She told me to leave."

Sam gave him an encouraging smile. "I'm sure Dr. Keller just wants him to get some rest. She'd let us know if there was a real problem."

"Yeah." He wasn't really convinced. "What can I do?"

She blew out a wear breath. "You can help Maj. Lorne."

"Okay."

"Come on." Lorne headed for the stairs with the Satedan close behind.

xxxxxxxxxx

Jennifer looked up at the sound of approaching footsteps. "Colonel?"

"Doctor." Sam nodded toward the next room, knowing Sheppard was in there. "How's he doing?"

"He's stable." Jennifer tapped the edge of the tablet resting in the crook of her arm. "How about you?"

It was obvious that Sam was ready to fall asleep on her feet. Every single person she'd seen the last couple of days was in the same condition. Come to think of it, she probably looked the about the same. Jennifer had tried to avoided mirrors lately.

"I'll be fine. It's nothing a good 24 hours sleep won't cure." Sam responded wryly.

"I think I'm going to be prescribing a lot of that in the next day or two." Jennifer said, only half joking. She saw Sam glance at the door again. "I really don't have anything yet. I'm still going over the scans and other tests. For the time being, Col. Sheppard's condition is stable and his vital signs are in the normal range for him."

"Ronon said he was unconscious."

"He is and he isn't. He isn't responding to normal stimuli, so he isn't just sleeping. But, he isn't unconscious, either. Not exactly, anyway."

"Excuse me?" Sam was too tired to try to follow that.

"I was able to run a scan when Ronon brought him in. The activity level was more intense than any of the earlier scans. Much more." She tapped on the data pad again. "His EEG…shows waves that are not normally associated with unconsciousness."

"Then why isn't he awake?"

"The EEG indicates John is dreaming, but he isn't exhibiting the physical activity typical with REM sleep such as rapid eye movement and muscle twitching. His mind is very active. It's just that his body is disengaged. Sorry, I don't have an explanation." Jennifer led her into the scanner room and brought up a set of images. Each was date and time stamped. She scrolled through them slowly. "I want you to see this. These are the scans I showed you the other day."

"What about now?"

She changed the images. "These, you haven't seen, and this one is from a couple of hours ago. I want to run another one in a few hours, but I'll have to see how he's doing first."

"What's going on?"

"To be honest, I don't know." The doctor threw up her free hand and sighed in frustration. "Each time I've been able to run a scan right after John was beamed here and then before he went back to the chair room, the rate at which the unusual synaptic activity diminished was slower. It has taken longer for it to return to normal every time. Actually, during the last couple of days, there hasn't been enough time. He's had significantly increased activity for more than 48 hours straight."

"Do you have any idea when he might wake up?"

"Sorry, no." Jennifer shook her head. "It's all up to him."

This worried the colonel. "What about long term effects?"

"This is a first. I don't know if the intensive use of the Ancient technology has made a permanent change to his brain. Right now, I think the only thing we can do is wait and see."

"You can't give him anything?"

She sighed. "I think it's best to do nothing while he's stable. I'm not sure if there would be any side effects from the painkillers or any other medication, and don't want to risk it if at all possible."

Sam's eyebrows went up. "Do you think it could cause more harm?"

"Probably not, but there are too many unanswered questions about what's going on that I'm reluctant to try it if I don't absolutely have to. I'll keep him hydrated and closely monitor him. If his condition deteriorates or he doesn't come around within 24 hours, I'll intervene."

xxxxxxxxxx

Jennifer's eyes went from the heart monitor to Ronon then to the tablet that seemed to have become attached to her since this started. She entered the numbers from the monitor then turned off the tablet. His vitals steadied soon after Ronon brought him to the infirmary and stayed that way for the last dozen hours.

She walked over to the Satedan and whispered, "You don't need to stay."

"I know." He replied so quietly that she barely understood the words. He'd quietly slipped back into the infirmary when Lorne scheduled him for a few hours sleep. The doctor relented and let him stay after a very short and intense stare-down.

Jennifer wasn't really concerned about waking her patient, and would have actually been happy if he came around for a minute. Until that happened she wouldn't be able to truly gauge how he was doing. The scans and EEG told her only part of the picture. This was a unique situation and she needed to talk to him to be certain.

"Okay. Call me if he stirs." Jennifer gently squeezed Ronon's shoulder and walked out. There was no need for Ronon to say anything, actually. Either she or one of her staff would be in the room at all times. John was the only patient, but even if the infirmary were full, it wouldn't change the fact that he needed close and constant monitoring. She nodded at Marie as she left, hoping another search of the Ancient database might turn up something that would help.

xxxxxxxxxx

McKay walked around the consoles in the control room, a steaming mug of coffee in one hand. He groaned as he sat in the chair. The long days of sitting at the computer hour after hour with few chances to move had stiffened muscles he never knew existed. He blamed Sheppard for it. His knack for getting them into situations where physical exertion was necessary to stay alive and in one piece resulted in the scientist being more physically fit than he'd been in his life. Being a geek was not easy any more. Gone were the days he was content, even happy, to sit at a computer for hours on end. His body, now used to getting fairly regular exercise, protested inactivity.

Everyone who remained on Atlantis was now able to get much needed sleep. Col. Carter ordered it as soon as they were reasonably certain that the place wasn't going to fall down. With the Apollo backing up the city's sensors and fire power, both civilian and military personnel were being rotated out on mandatory six hour rest periods. She wanted to ensure that her people didn't fall down, either.

He stopped with the mug halfway to his mouth, thinking. Sheppard collapsed almost fifteen hours before. In that time, diagnostics were run, Radek had written a program to sniff out Earth based computers, McKay looked it over and they ran it. No-one knew whether it was a good thing or not, but just the one computer found by Sgt. Simmons appeared to be the culprit. Just to be sure, though, at least one more physical sweep would be done, and Rodney decided to beef up the Czech's program and run it again. It would take time, but it had to be meticulous.

Sheppard was still unconscious, asleep, whatever. McKay frowned at the thought that Jennifer still didn't know what was going on in that stubborn head. She allowed him only a quick peek in as he made his way to his quarters earlier. The room was almost too dark to see anything, but he saw enough to know his friend wasn't just sleeping. That, with the obvious concern of the doctor and her staff for their only patient, was distressing.

Col. Carter's sudden appearance jerked him out of his thoughts. "Rodney, did you get any sleep?"

"A couple of hours." Blinking with still bleary eyes, he looked around. "I take it the city didn't fall apart while I was asleep?"

"Nope." She smiled, relief in her answer. "Diagnostics are still running, but we seem to be in good shape."

"Good. I'm going to write a program to search for viruses or anything else that shouldn't be in the programming. I should have it finished later today."

"That's a good idea." Sam said then shook her head thoughtfully. "I didn't think we'd have to watch out for an attack from Earth."

"Well, the bad guys aren't restricted to the Pegasus Galaxy." Rodney observed dryly.

"No, that's for sure." She said as she walked around the console to sit at her computer. "We'll wait until we've run your program before bringing everyone home."

xxxxxxxxxx

There were only two jackhammers in his head now and the darkness was no longer quite as black. John had the feeling he needed to be someplace but he couldn't remember where or why. And, for some reason, he wasn't worried about it. It would come back. He just had to give it a little more time. At least it felt safe now. He didn't know why, but it finally felt safe to climb out of the hole.

"Colonel?"

The urgent tone gave John the sudden feeling he had to wake up. There was something important he had to do. What the hell was it? His brain objected to the need for information, the need to think. He sensed more than heard deliberately quiet movement coming closer.

"John?" The voice wasn't much more than a hopeful whisper now. Something cool touched…what was that called again? Face. It touched the side of his face. "John?"

He opened his eyes just enough to see a shape bending close to his face. Was it talking to him?

"John, can you hear me?"

"Hnn?" The croaking sound seemed distant.

The shape moved, letting a dim light shine in his eyes. He tried to turn away, but something was stopping him. It held him and he couldn't move it. Even raising a hand to shield his eyes was nearly impossible. John groaned softly.

"I'm sorry." Jennifer moved back to block the light. He was still propped on his side by pillows, and couldn't escape the glow.

"Is he awake?" Ronon leaned across the bed in an effort to see his friend's face then walked around it.

She kept her attention on her patient. "Yes, just now."

Sheppard knew he was supposed to be doing something other than just laying there. It took a moment to realize that Ronon was nearby and it shook loose the memory he sought. He slowly moved his hand and found the bed rail. At least the hand was moving, he thought. Isn't it? It was difficult to tell.

"Gotta…" was all he could get out.

"No. No. No. You're not going anywhere." She said quietly, taking his hand and deftly moving her fingers to check his pulse.

"City. Need to..." He tried to move again but couldn't find his body.

"The city is fine, John. You did it." She tried to reassure him.

Didn't she understand? "Wraith."

"The Wraith are gone. Everything's okay." This time Ronon stopped him, needing no more than the gentlest pressure. He squatted low so that Sheppard could look straight at him. "They fixed the computers."

"Sure?" John tried to wet dry lips.

"Yeah. Carter said it looks good. She and McKay are keeping an eye on things."

John peered at him for several seconds, trying to get his sluggish brain to work faster and his eyes to focus. His mouth and throat were too dry to swallow and the only sound he could make was a hoarse cough.

"Would you like a little ice?" Jennifer asked. It was a moment before he nodded. She carefully slipped a small piece between his lips. He let it melt and took another, closing his eyes as the water soothed his mouth and throat.

"Thanks." The cold liquid helped to clear his head a little and he was thinking in something resembling real time again. "It worked?"

"Yes, it worked." Jennifer offered another ice chip which he took.

"They're going to start bringing everyone back from Midway soon." Ronon added.

"Good." John said as his eyelids began to close. They jerked open again and he frowned at Ronon, who was still at eye level. "You sure?"

The Satedan smiled and nodded. "Yeah, buddy. We're good."

"'Kay." This time he couldn't stop himself drifting off to sleep.

Jennifer watched the EEG closely.

"Is he okay?" Ronon looked from the monitor to her back to Sheppard.

"He's better. I'll need to see more, but it looks more normal." She nodded, marginally happier with what she was seeing. She put on her stethoscope and listened to his heart and lungs, gently maneuvering the instrument between the sleeping man and the pillows. She glanced at Ronon, who frowned at his friend. "Look, John woke up and was lucid. He remembered what happened. And, he did it a lot faster than I thought possible."

Ronon watched in silence while Jennifer finished her exam. She motioned the nurse to come over while she guided him away.

"He'll probably be asleep for some time." She said, but could tell he wasn't convinced. "It really does look like John is sleeping, and that is exactly what he needs right now. You look like you could use some yourself."

"I'm fine." He rumbled.

"I know, but all the same, you should get some rest." She thought for a moment. "Why don't you go let Rodney and Col. Carter know that John woke up. I'll call you if he wakes up again. Okay?"

Not taking his eyes from his friend, he considered her suggestion for several seconds. To her relief, he nodded. "Okay. You'll let me know?"

"I promise." She replied with a reassuring smile.

xxxxxxxxxx

This time, awareness was instantaneous and jarring. John woke with his heart pounding and in near panic, but didn't know why. He tried in vain to push himself up on rubbery arms.

"Wait. Where do you think you're going?" Dr. Cole hastily set down a data tablet and put her hands on his shoulders.

"Have to go." His voice was raspy with dryness. He gulped breaths as he tried to push her away, becoming dizzy with the effort. "Wraith…coming."

"No. No. They're gone, Colonel." She tried to reassure him.

"They're gone. The Wraith left yesterday, John." Dr. Keller suddenly appeared on the other side of the bed.

He licked his lips, blinking in an attempt to focus on her. "Yesterday?"

A small smile appeared to ease his anxiety. "About eighteen hours ago. They didn't find anything here so they left."

He closed his eyes and stopped struggling. Both women could see he was still in considerable pain despite the full day since Ronon brought him in. They thought he was sleeping again when he asked, "Sure?"

"Quite sure. Col. Carter has even brought back everyone that stayed on Midway after the evacuation." Jennifer tried again to reassure him. It seemed to work this time. He relaxed, nodding once.

"Jennifer?" Dr. Cole raised an eyebrow at her colleague.

"Yes." She responded without looking up. "John? I want to run a scan. Are you up to it?"

His cringed inwardly at the thought of moving but nodded. "Yeah."


	12. Chapter 12

**Chapter 12**

"Uh, sorry. I'll come back later." McKay hesitated, not really wanting to leave.

Jennifer looked up from her tablet as Alex finished straightening the blanket over Sheppard. After a quick glance at her patient, she waved him in. "It's okay. Come in."

He didn't move until Alex stepped back and he saw Sheppard looking in his direction. The colonel nodded once and a tired smile appeared on his face. Rodney took a deep breath and went over to him. The room was dimly lit and the head of the bed was raised slightly.

"Everything okay?"

"Yeah, as far as we can tell." The scientist fidgeted. He found it hard to see his friend in this condition. John looked quite ill and several days growth of dark beard accentuated the pallor. The affects of the pain were too obvious to ignore. He anxiously glanced at the doctor. "Is it okay to talk for a few minutes?"

"A few." She raised a warning eyebrow at him and spoke in a near whisper. "As long as you promise to be quiet."

"Of course. Quiet. I promise." Rodney readily agreed. He knew full well what his outbursts had done to his friend.

Jennifer picked up a glass of water with a straw. Not wanting to risk John's unsteady hands, she raised the head of the bed a little more and held the glass for him. He slowly took a couple of sips.

"Thanks." His voice sounded foreign and rough, but at least it was intelligible.

"I'll be right back." The doctor put the glass back on the bedside table and left them to talk. The nurse followed her out.

"Wraith?" A fear he wouldn't be able to help if they returned was just below the surface.

"The entire fleet left close to 26 hours ago." Rodney saw his uncertainty. "We're pretty sure they're convinced this planet is deserted."

"Where…," his voice cracked. He cleared his throat before trying again. "Where are they?"

"It looks like they're en route to a system on the same general course. The direction is close enough that it could be mistaken for the source of the beacon. They'll arrive in about eighteen hours."

John's eyelids drooped. He pressed his fingers against them then blinked exaggeratedly, trying to clear his vision. He looked back up at Rodney. "Inhabited?"

"Are you okay?" Rodney didn't like what he was seeing.

"Yeah."

"Okay. It was inhabited but the settlement was abandoned after a storm just about destroyed it. We sent a team to confirm no-one remained and left a device among the ruins that generates the same beacon sent by Atlantis." Rodney grinned with not a small amount of smugness. "I thought of that."

"Good idea. They'll fall for it?" He pressed the area above his right eyebrow and temple, trying to ease the persistent ache. Even though it wasn't quite as severe, the migraine was still vicious.

"I think so. I made sure the device was sufficiently battered. It'll appear that the storm set it off." Rodney saw him lose even more color. "I should get Jennifer."

John held up a shaky hand to stop him. "No. I'm fine. Everyone back?"

"No, we're still running diagnostics and verifying code. We'll probably recall those who stayed on Midway in a little while. Only a couple of dozen are there. Sam wants to run a full systems check before we let everyone who went on to Earth come back." He didn't go on to say they wanted to have Sheppard in the chair for that.

John rubbed his forehead with trembling fingers. There was something he was forgetting. It finally came back, or at least part of it. "The planet we thought the Wraith were going to. What happened?"

"M5Q-491? We think it's safe for the moment. The Wraith seem to have forgotten about it. The people are prepared to evacuate if necessary. We'll watch for any indication the Wraith change course for the planet and the away team is still there if anything changes." Rodney leaned forward. Something was definitely wrong.

John found the EEG pad on his right temple then felt the left. He peeled them off, causing the monitor to beep softly.

"What are you doing?" Rodney was alarmed by the action.

Dr. Keller hurried in, closely followed by Alex. "That's what I want to know.

Rodney stepped back. "What's wrong?"

"It's the headache." She said as if it explained everything. She automatically checked the heart and blood ox monitors then turned off the EEG monitor. "Okay. We can leave that off for now, but I want you to get some sleep."

"Can't you give him anything for it?"

"Don't need anything." John glared at them with hooded eyes.

"I know." She said softly. The possibility of an adverse reaction made her reluctant to override his resistance. There was also still some uncertainty about the stability of the city's computer system. If it went offline again, Sheppard needed to be as clear headed as possible, as if his current state was at all clear headed. She looked at McKay. "Would you excuse us, please? I'll let you know when you can see him again.""

"Of course." He reluctantly back away. "I'll…see you later."

John nodded once and closed his eyes. He was trying to breathe deep and slow to ease the pain but it wasn't working.

Rodney stopped at the door and looked back to see her rest her hand on his forehead and lean in close. Her voice was just audible. "Still bad?"

"Yeah." Then he said something Rodney couldn't understand.

He watched as Jennifer and Alex lowered the head of the bed then helped him turn onto his side, making sure the IV tube and monitor leads didn't get tangled. Rodney could see the movement was difficult. Suddenly feeling he was intruding on a vulnerable moment, he turned away.

xxxxxxxxxx

Rodney wasn't willing to just leave without knowing more about Sheppard's condition. He knew he should be heading back to the Gate room, but couldn't go yet. He walked into the scanner room and dropped into the chair at the controls. It didn't take long for him to need something to do.

Pulling the chair up to the computer, Rodney turned it on. He peered at the screen, reading the data accompanying the image. Without thinking, he slowly scrolled through the file, studying each image, the device's interpretation of the data and the doctor's notes.

"Oh, my god." He whispered.

"Rodney!" Jennifer exclaimed. He jumped as she hurried towards him. "What are you doing?"

"What is this?" He pointed to the monitor. "Is this Sheppard?"

She glared at him as she turned it off again. "Yes. It is. And you shouldn't have been looking at it."

"I thought you said he was getting better. Those scans don't look like it." He demanded in a hushed tone and pointed to the other room. "John doesn't look like it."

"John has improved, Rodney. The scans show his synaptic activity is returning to normal. It's slow, but it is." She explained, understanding his anxiety. She continued as they walked to her office. "The pain is still very severe, but it isn't as bad as it was when he first woke up yesterday. His vision has also improved."

"Well, it doesn't…" he stopped and stared at her. "Vision? What do you mean?"

"Rodney, the pain was bad enough to cause near blindness." She sat down at her desk. "Even though he wouldn't admit it, I know John's vision was getting worse over the last couple of days. It's similar to many severe migraines. I just didn't know how bad it had gotten or if it was temporary."

Stunned, Rodney dropped into another chair. "Is it? Temporary, I mean. Is it temporary?"

"I am hopeful. Like I said, it's improving. We'll have to wait and see."

xxxxxxxxxx

"Ready?" Sam raised an eyebrow at Rodney.

He swallowed hard and nodded. His attempt to put confidence in his voice didn't quite work, and he squeaked, "Ready."

She took a deep breath and turned to Chuck. "Dial it."

"Yes, Ma'am." He replied as he started the dialing sequence.

Even the kawoosh of the opening wormhole didn't allow the people in the Gate room relax. Each of them watched the puddle with a wary eye. Those in the control area nervously checked computers for any hint of trouble.

"Midway, this is Col. Carter."

"This is Dr. Lee. It's good to hear Atlantis is back online, Colonel." The scientist's disembodied voice echoed the tentative relief in the Gate room. Lee had been sent to the space station to offer any assistance possible. They all knew there was very little he might be able to do, but Gen. Landry wanted all bases covered.

"Thank you, Bill. We're sending a MALP through to test the wormhole's stability. I want you to send it back. If all goes well, our people can start coming home."

"Very well, Colonel. We're ready to receive the MALP."

xxxxxxxxxx

"It's good to have you back, Teyla."

"Thank you, Colonel. It is very good to be back." The young Athosian smiled and bowed her head then the smile disappeared. "How is Col. Sheppard?"

"The doc says he's sleeping." Ronon frowned.

"Sleeping?" She heard something in his voice that said it was not really sleep. "Is he alright?"

He shrugged. "She thinks he's getting better."

That did nothing to dispel their doubt. Sam bit her lip, thinking about her 2IC. "I'm sure he'll be fine. Jennifer said the best thing was for him to rest."

Ronon leaned against the console where Sam and Rodney were sitting. "He knew something was wrong."

"Excuse me?" Sam asked.

Rodney shook his head in disbelieve. "Oh, please. I know Sheppard…"

"He knew something was wrong." Ronon repeated. "Right before…"

"How could he know?"

"We were down on the south pier. Right before everything went down..." The Satedan paused for a moment. This sounded crazy, but it was too late. He'd said it. "John suddenly stopped, said 'What the hell?' and took off. It's like he knew something was wrong before it happened."

"John was acting quite oddly for several days." Teyla immediately accepted the idea.

Rodney tried to dismiss it. "Oh, please. Sheppard isn't psychic. He couldn't have possibly known."

"He is uniquely attuned to the city." Sam shrugged. Stranger things had happened in her years with the Stargate program. "The minor malfunctions in some systems in the days leading up to everything crashing were probably caused by the viruses. John may have been picking up on that."

"It would explain his behavior." Teyla said thoughtfully.

"Is that possible?" Even though he'd seen it, Ronon was skeptical.

Rodney wasn't at all comfortable with the thought. "No. Is it?"

Sam exhaled heavily. She decided not to recount the analogy John gave her about flying. Only a pilot would truly understand it. Instead, she reminded him of his own statement. "Rodney, you yourself said something was missing when you tried to activate the systems. Given his natural abilities with the Ancient technology, would it be possible that John feels that more acutely?"

He scowled at the computer in front of him before conceding, "Yeah, I suppose."

xxxxxxxxxx

"Are you sure he is up to visitors?" Teyla asked the doctor. She glanced at Ronon, who was standing at the doorway to Sheppard's room, looking in. "Rodney said John was in a great deal of pain. I would not want…"

Jennifer held up a hand to stop her. "Yes, he was, but he's gotten a few more hours' sleep, and I think hearing from Rodney that we were out of danger helped. The combination of the lights, doing another scan and moving him around didn't help. John slept much better last night, and really is better."

"Is his brain activity returning to normal?"

"Yes. The scans are showing improvement. It's happening much slower than I hoped, but it's getting there."

"Is there any danger of long term effects?" The young Athosian was fearful. She saw so little of him in the days before leaving for Midway. He'd looked dreadful the last time she saw him.

The doctor tapped the tablet cradled in her arm. "Look, this is all new to me. I've searched the Ancient database, but can't find any similar incidents. I hope not, but I don't know."

"When will you know?" Ronon's expression was dark when he turned to look at her.

"I hate to keep saying this, but I don't know." Jennifer shrugged helplessly. "I'm hopeful he'll fully recover. Sleep is the only treatment I can think of right now. To put it very simply, short of deep sedation, sleep is the closest thing to resting his brain as we can get. John won't let me sedate him, and I wouldn't want to go that route, anyway."

She could see their doubt.

"I think it's taking longer to get back to normal for a couple of reasons. First, the brain is active to one degree or another during sleep. Second, John was using the chair for a very long period and supporting the entire city pretty much the whole time. His synaptic activity went back to normal the first couple of days because he had longer breaks between sessions in the chair. After that, he spent more time in the chair and less resting, as well as keeping the Gate active twice."

Teyla wasn't satisfied. "John has never had any kind of adverse reaction to using any of the Ancient technology. It is normally effortless for him. Why was the reaction so severe?"

"I believe it was the amount of time and the enormous effort he put into it. I'll keep searching the database for any information that could help, but..." The doctor sighed in resignation.

"Perhaps we should come back another time." Teyla glanced towards the door.

"I don't think a few minutes will hurt. Besides, he's a bit restless. I think he'd appreciate the company. Just remember he's tiring easily." She walked into Sheppard's room with them. "Feel like a couple of visitors?"

Teyla immediately noticed the lights were slightly brighter and Sheppard's color was closer to normal than Rodney described. There was pain in his eyes, but not as much as the last time she saw him, and they were properly focused for the first time in days. He was sitting up in the bed and the monitors were disconnected and silent. Only the IV was still there.

He seemed pleased to see them. "Sure."

"How are you, John?" Teyla smiled warmly.

"I'm good." He put a water glass on the table next to the bed.

"I'll let you guys talk. Ten minutes." Jennifer said and she left.

"Thank you." Teyla accepted the chair Ronon pulled closer and sat down. "It is very good to see you. Jennifer says you are getting better. Are you?"

"Yeah. I'm good." He cocked his head slightly to one side. "When did you get back?"

"Only a short time ago, and I am very happy to be home." She glanced at Ronon, his unreadable expression was slightly disturbing. She knew the Satedan had been deeply worried for their friend. "I…I understand that Col. Carter does not want the personnel who went on to Earth to return just yet."

He vaguely remembered someone telling him already. "Um…Rodney told me. I think. Everything's working okay?"

"Yes, I believe so." She looked around. "It appears to me that all is well, thanks to you."

John shrugged then looked up at Ronon. "Lorne has everything under control?"

"Buttoned up tight."

"The Apollo remains as well. Col. Ellis delayed their departure until we are certain all systems are functioning normally and free of the virus."

John absentmindedly scratched his cheek. Seeming to realize there was a substantial growth of beard, he frowned. "How long…?"

Teyla immediately understood what he wanted to know. "The viruses attacked the computers nine and one half days ago. You have been here in the infirmary almost two."

He blew out a silent whistle. "Crap."

xxxxxxxxxx

"I've been running scans every twelve hours or so." Jennifer explained as she called up a series of images showing the progress of the changes in Sheppard's brain. Col. Carter and Dr. Reynolds studied each one intently. "The first is the one I showed you from his physical three months ago, Sam. Then you can see where we started ten days ago, and each scan since."

"The activity is diminishing, even if slowly." Beth read the data accompanying each image. The slides from the last two days of the crisis were both fascinating and worrying. The half dozen run since the computers were brought back on line were only slightly less so. "Do you think it will return to normal?"

"I think so, or at least close to normal." Jennifer responded as the latest scan appeared on the monitor.

"And, if it doesn't?" Sam wondered aloud, turning to the young doctor. "What would it mean? Would the headache continue? Any other side effects?"

"I don't even want to speculate." Jennifer turned off the computer. "Like I've said, this is all new. I'm still trying to figure out why the activity increased, and to the extent it did."

"When are you going to release him?" Beth asked as she continued to stare at the image.

"I'm going to run another scan this afternoon. I'll let him go right after that if he continues to improve. I'll keep a close eye on him until I know…more." She finished with a frown, realizing she didn't know how long that would take.

Sam compressed her lips, also understanding the uncertainty of the situation. She nodded. "Just keep me informed."

xxxxxxxxxx

Relieved to see the mess hall was deserted, Dr. Reynolds headed for the coffee urns. It was late and she just wanted a cup of the strong, black brew and some air before getting back to her reports. It was only when she walked out to the balcony that Beth spotted Sheppard sitting alone in a darkened area. It was nearly 0130, far too late for him to be here.

She was grateful it was the time of night when the prior watch had already eaten dinner and gone to quarters or elsewhere to wind down. The current watch wasn't due for meal breaks just yet and the next watch wouldn't stir for a few hours.

She approached him. Staring out over the city, he was oblivious to her presence. A half full glass of juice and a bowl of crackers on the table in front of him seemed to be forgotten. She paused, suddenly uncertain whether she wanted to disturb his thoughts. Seeing him draw in and slowly exhale a deep breath made her regret the unplanned intrusion. That was the sigh of someone trying to shake something off. Before Beth could quietly retreat, he looked up at her.

A shadow of disappointment passed so quickly over his face she wasn't even sure she'd seen it. His typical relaxed expression appeared. He had shaved but still appeared tired, not unexpected since Jennifer released him from the infirmary only a few hours earlier. He glanced around the empty space before speaking. "Doc?"

Beth decided not to try to put on her bedside manner. He would immediately see through it. Honesty and openness was advised here. "I'm surprised to see you up at this hour, Colonel. I thought Dr. Keller wanted you to rest."

"I've been sleeping for three days. I feel like Rip Van Winkle." He observed humorlessly and let his eyes swept over the city again. "I needed to get some fresh air."

"Yes, of course. You have been stuck inside for a while, haven't you?" Beth knew Sheppard hadn't been outside for more than a few minutes in at least ten days. This was his first chance to be alone and think in that time as well. "I'm sorry I disturbed you."

"That's okay. What are you doing here at this time of night?" The question surprised her. It was an indication he was open to talking.

"May I?" She nodded towards the chair opposite him at the table.

"Sure."

"Reports." She slid easily into the chair. "That's what I'm doing up. I need to finish paperwork for the dial in to Earth tomorrow."

He nodded sympathetically. "I'm supposed to write a report about…" he finished by waving around one hand and rolling his eyes skyward.

She chuckled sympathetically. That was going to be a difficult report. "Good luck."

"Thanks." John frowned and scratched the back of his head. "I was sitting in the dark or sleeping most of the time so it's going to be full of holes."

"The others will be able to fill those in for you." Beth reminded him.

He merely nodded, his eyes wandering back to the glittering city laid out before them. Paris would be jealous, she thought. It was a truly awe-inspiring sight. She watched him out of the corner of her eye as a surprisingly easy silence fell between them.

Beth took the opportunity to study him. The tension and restlessness were gone, but the change from their last meeting was more than that. She was suddenly struck by how completely still he was right now, something quite unusual for the colonel. It was difficult for her to tell if it was just weariness or he was deep in thought. She decided a little of both. Jennifer mentioned the migraine was not completely gone and the latest scan showed the extraordinary synaptic activity, while diminishing, persisted.

Hoping to get a sense of how he felt, she didn't let the silence continue too long. "I heard that Col. Carter and Dr. McKay are fairly confident the virus has been completely eradicated. That's good news."

"Hmm." He slowly dragged his gaze from the view and blinked at her. "Sorry. Yeah. They're still checking it, I think."

"Of course." She watched him as closely as she could in the dim light. "Ronon believes you knew the city was in trouble before it happened. Did you?"

John winced inwardly, knowing everyone already thought he was losing it. He scratched his head again. "Maybe. I knew something was wrong, but not what. Not exactly."

She picked up on his sudden discomfort. "Don't worry. I'm actually happy to hear that."

That made him suspicious. "What do you mean?"

"I believe it goes a long way to explain your behavior in the days leading up to the system crash. Sam and Rodney think the viruses were causing problems for several days. You must have sensed it, for want of a better word."

"I don't have any special spidey sense, you know." He rolled his eyes.

"Well, I don't know about that." She grinned. "Seriously, though, you have a unique, and strong, sensitivity to Ancient technology. From what I understand about how it works, I would've been surprised if you didn't sense something was wrong. It's a remarkable ability, John."

He shrugged off the observation and drained the glass of juice. The reaction didn't surprise the psychologist. Sheppard was the polar opposite to McKay's need for self promotion. She felt John probably never consciously thought about his abilities as a pilot or with the Ancient's technology. It was as much a part of him as walking or breathing and required no attention.

She also suspected John didn't want to delve too deeply into what he'd experienced. She remembered Rodney and Evan reporting a dead feeling to the technology. Their description was disturbing. Beth couldn't imagine what it must have been like for John to work in that for so many hours and the thought made her shudder.

She knew his body, brain and mind were still recovering from holding Atlantis together for so many hours but needed to ask, "How does it feel now?"

"The city?" He seemed surprised by the question.

"Yes. And you."

His eyes narrowed, but Beth wasn't sure if he was thinking of an answer for her or reaching out to feel the city. After a couple of seconds, he exhaled a deep breath and looked her in the eye. Even in the semi-darkness, the directness of his gaze was disconcerting.

"What the hell are you dong here?" Rodney startled both of them with his sudden appearance. He was still a few meters away but made sure he was heard. He carried a sandwich and mug of coffee. "You're supposed to be taking it easy, remember?"

John sighed then raised an eyebrow. "I'm just talking to Dr. Reynolds. And, I am taking it easy. Why are you here?"

"I got hungry. Fixing a mess that big in the computer system takes time and energy you know." The physicist sat down at the end of the table. "It's the middle of the night. Shouldn't you be in bed?"

"Just getting some fresh air, Rodney." He replied lazily.

Beth took this as her cue to leave. McKay looked like he was anxious to talk with his friend. She stood up, looking at John. "I guess it's time to get back to my paperwork. Gentlemen."

He caught her eye before she turned to leave. "What you asked before. Good. On both counts."

Her mouth formed a silent "O" before a pleased smile appeared. "I'm very happy to hear that, John. Thank you. Goodnight."

Rodney watched the doctor walk away then turned to him. "Good? What's good? What did she ask?"

"Nothing, Rodney. I thought you said the programming was fixed."

"Well, it is, but someone needs to go through what the people laughing called programmers did during this mess." McKay bit into his sandwich, chewed a couple of times then continued. "I've…mmm…to clean up a couple of iffy…mmm…in two subroutines. I wish the SGC would send…mmm…literate people. They're all morons."

"No they're not." John chided him gently. He knew Rodney, Sam Carter and Radek, as well as many others, pulled off an amazing feat. By all rights, Atlantis should be radioactive vapor.

Not one to willingly give praise to anyone else, Rodney shot back, "Well, I did most of the work, anyway. You have no idea what I have to put up with. They send me…"

John let Rodney carry on the one sided conversation as his gaze wandered back to the city. Zoning out the long-winded astrophysicist while knowing when to nod or agree was easy. Rodney didn't need anything more than a live body giving the appearance of listening. He was happy to do all the talking.

The headache considerably improved but still lingered. Jennifer released him from the infirmary only after one of the most thorough medical examinations he'd ever experienced. John's last scan showed significant elevated brain activity remained but she was fairly confident he would return to normal over time. The doctor wanted to check him daily until it did, so John was to present himself again at 1100 hours the next morning for the first scan. Much to his chagrin, Teyla and Ronon assured Jennifer he would be on time.

His vision was already near normal. It wasn't quite good enough to read yet, but he was enjoying the view. John decided he didn't need the year to pass judgment on the night sky here. Cloudy or clear, it would do just fine.

"Are you listening to me?" McKay's miffed tone broke through his thoughts. "I said I was sorry."

"Hmm? Sorry about what?" John blinked at him.

"For yelling." Rodney's annoyance softened immediately. "I'm sorry I yelled at you the other day, and…before…that."

John paused, not quite remembering what he was talking about, but an admission of guilt out of McKay was rare. He let the silence stretch out, rubbing his chin as if considering the offered apology. He finally sighed exaggeratedly, "Okay. You're forgiven."

Rodney eyed him critically then pushed back his chair. The apology was accepted too quickly, too easily. He could also see his friend was tiring. "Right. I don't want Keller to blame me for keeping you up all hours. Come on."

Sheppard let his eyes take in the city one last time. It had been close, too close, he thought. Again. One day, they might not be able to save her.

Rodney saw the pensive expression, followed John's gaze and understood. "Yeah. I don't want to do that again."

"No." John sighed wearily.

"Hey, come on. The sooner you get your head together, the sooner I can run a complete systems check." Rodney frowned at him. On seeing John's momentary confusion, he explained, "Remember? Sam won't let me do it until Jennifer clears you to use the chair."

"Oh, yeah." He pushed his chair back and stood up.

Rodney grabbed his coffee mug and stood as well. He hesitated, peering closely at his friend. "When you're ready, of course."

The End

Of this one, anyway…


End file.
